Differential regulation of mRNAs and lncRNAs related to lipid metabolism in two pig breeds

Exploration of non-coding RNAs related to intramuscular fat deposition Xinjiang Brown cattle and Angus × Wagyu cattle

Non-coding RNAs (ncRNAs) serve as crucial regulatory elements in the process of adipogenesis in animals; however, the specific roles and interrelationships of ncRNAs in bovine fat deposition remain poorly understood. This study aims to investigate the differentially expressed ncRNAs in the longissimus dorsi muscle of Xinjiang Brown cattle (XB) and Angus × Wagyu cattle (AW), to elucidate the regulatory mechanisms underlying lipidogenesis that may involve ncRNAs. Four Xinjiang Brown cattle and four Angus × Wagyu cattle were selected, ensuring they are subjected to identical feeding conditions, in order to evaluate the intermuscular fat (IMF) of longissimus dorsi muscles. The fat content of muscle tissue was quantified using the Soxhlet extraction method, revealing that the fat levels in the AW group were significantly elevated compared to those in the XB group. Taking muscle samples for paraffin sectioning and observing their morphology, it was found that the fat richness of the AW group was significantly higher than that of the XB group. Utilizing high-throughput RNA sequencing technology, we conducted an extensive transcriptomic analysis of longissimus dorsi muscles of XB and AW to identify significant ncRNAs implicated in fat metabolism and adipogenesis. The miRNA analysis yielded between 109,343,831 117,258,570 clean reads, whereas the lncRNA and circRNA analyses produced between 81,607,756 102,917,174 clean reads. Subsequent analysis revealed the identification of 53 differentially expressed miRNAs, 176 differentially expressed lncRNAs, and 234 differentially expressed circRNAs. KEGG enrichment analysis revealed that the target genes of differentially expressed miRNAs, lncRNAs, and circRNAs are significantly enriched in 2, 17, and 22 distinct pathways, respectively. The pathways associated with the differential enrichment of miRNA target genes involve processes such as phosphorylation and protein modification. Concurrently, the pathways linked to the varying enrichment of lncRNA target genes encompass G protein-coupled receptor signaling, regulation of cell death and apoptosis, activities related to GTPase activation, and functions governing nucleotide triphosphatases, among others. The circRNA exhibiting differential expression are significantly enriched in a variety of biological processes, including signal transduction, nucleic acid synthesis, cellular architecture, GTPase activation, and phosphatase activities, among others. The analysis of the ncRNA interaction network suggests that AGBL1, THRB, and S100A13 may play pivotal roles in the formation and adipogenic differentiation of adipocytes. In conclusion, we conducted a comprehensive analysis and discussion of the complete transcriptome of intermuscular fat tissue from the longissimus dorsi muscles in Xinjiang Brown cattle and Angus × Wagyu cattle. This study provides a theoretical foundation for enhancing our understanding of the molecular mechanisms underlying fat metabolism and deposition in beef cattle.

Non-Coding RNAs in Regulating Fat Deposition in Farm Animals

Fat deposition represents a crucial feature in the expenditure of physical energy and affects the meat quality of farm animals. It is regulated by multiple genes and regulators. Of them, non-coding RNAs (ncRNAs) play a critical role in modulating the fat deposition process. As well as being an important protein source, farm animals can be used as medical models, so many researchers worldwide have explored their mechanism of fat deposition. This article summarizes the transcription factors, regulatory genes, and signaling pathways involved in the molecular regulation process of fat deposition; outlines the progress of researching the roles of microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) in fat deposition in common farm animals including pigs, cattle, sheep, ducks, and chickens; and identifies scientific problems in the field that must be further investigated. It has been demonstrated that ncRNAs play a critical role in regulating the fat deposition process and have great potential in improving meat quality traits.

Identification and Co-expression Analysis of Differentially Expressed LncRNAs and mRNAs Regulate Intramuscular Fat Deposition in Yaks at Two Developmental Stages

Intramuscular fat (IMF) content is a key indicator of yak meat quality. This study aimed to identify lncRNAs that regulate IMF deposition in yaks. Three male calf yaks (3 months) and three male adult yaks (3 years) were used in the current study. After slaughter, the tissue morphology of the longissimus dorsi (LD) muscle was assessed using a cry-sectioning technique and differentially expressed lncRNAs and mRNAs (DELs and DEMs) were identified using RNA-Seq technology. The diameter and volume of fat droplets were significantly larger and bigger, respectively, in adults than in calves (P < 0.001). A total of 37,790 genes and 16,400 lncRNAs that regulate fat deposition were identified. Among them, 2327 mRNAs and 474 lncRNAs were differentially expressed between calves and adult yaks. DEGs stearoyl-CoA desaturase (SCD), fatty acid synthase (FASN), fatty acid binding protein 4 (FABP4) and fibronectin 1 (FN1) and DELs MSTRG.15795.4 and MSTRG.35028.6 were screened. The enrichment and pathway analysis regulated by the DMEs and DELs were predicted. We found significantly enriched biological processes and pathways involved in fat deposition, including the biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, fatty acid elongation, and the mTOR signaling pathway. Co-expression network of the DELs and related genes, including MSTRG.10268.1-placenta associated 8 (PLAC8), MSTRG.16223.1-galectin 3 (LGALS3), MSTRG.34732.1-glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), MSTRG.11907.11-fibroblast growth factor 1 (FGF1), MSTRG.34342.1-lipase A, lysosomal acid type (LIPA), and MSTRG.1667.2-integrin subunit beta 2 (ITGB2) was constructed. RT-qPCR verified the sequence results. The molecular regulatory mechanisms of lncRNAs on intramuscular fat deposition in yak were further explored.

Transcriptome Analysis Reveals the Early Development in Subcutaneous Adipose Tissue of Laiwu Piglets

Adipose tissue plays an important role in pig production efficiency. Studies have shown that postnatal development has a vital impact on adipose tissue; however, the mechanisms behind pig adipose tissue early-life programming remain unknown. In this study, we analyzed the transcriptomes of the subcutaneous adipose tissue (SAT) of 1-day and 21-day old Laiwu piglets. The results showed that the SAT of Laiwu piglets significantly increased from 1-day to 21-day, and transcriptome analysis showed that there were 2352 and 2596 differentially expressed genes (DEGs) between 1-day and 21-day SAT in male and female piglets, respectively. Expression of genes in glycolysis, gluconeogenesis, and glycogen metabolism such as pyruvate kinase M1/2 (PKM), phosphoenolpyruvate carboxy kinase 1 (PCK1) and amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase (AGL) were significantly different between 1-day and 21-day SAT. Genes in lipid uptake, synthesis and lipolysis such as lipase E (LIPE), acetyl-CoA carboxylase alpha (ACACA), Stearoyl-CoA desaturase (SCD), and 3-hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) were also differentially expressed. Functional analysis showed enrichment of DEGs in transcriptional regulation, protein metabolism and cellular signal transduction. The protein-protein interaction (PPI) networks of these DEGs were analyzed and potential hub genes in these pathways were identified, such as transcriptional factors forkhead box O4 (FOXO4), CCAAT enhancer binding protein beta (CEBPB) and CCAAT enhancer binding protein delta (CEBPD), signal kinases BUB1 mitotic checkpoint serine/threonine kinase (BUB1) and cyclin-dependent kinase 1 (CDK1), and proteostasis-related factors ubiquitin conjugating enzyme E2 C (UBE2C) and cathepsin D (CTSD). Moreover, we further analyzed the transcriptomes of SAT between genders and the results showed that there were 54 and 72 DEGs in 1-day and 21-day old SAT, respectively. Genes such as KDM5D and KDM6C showed gender-specific expression in 1-day and 21-day SAT. These results showed the significant changes in SAT between 1-day and 21-day in male and female Laiwu pigs, which would provide information to comprehensively understand the programming of adipose tissue early development and to regulate adipose tissue function.

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

BACKGROUND

During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted.

RESULTS

Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. CONCLUSIONS: We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

Competing endogenous RNA network construction based on long non-coding RNAs, microRNAs, and mRNAs related to fat deposition in Songliao black swine

China has a long history of pig breeding and a number of local breeds. The Songliao Black pig, bred in China in 2009, shows high variation in backfat thickness and therefore is well-suited to fat deposition research. Fat deposition is a complex trait, and the underlying regulatory factors are not fully characterized. In this study, the molecular basis of fat deposition traits was evaluated by comparisons between three individuals with extremely high-backfat thickness and three with extremely low-backfat thickness selected from 53 gilts. Subcutaneous adipose tissues of the back were collected for strand-specific library RNA sequencing (RNA-seq) and small RNA-seq. We identified 13 184 mRNAs, 2046 long non-coding (lnc)RNAs, and 494 micro (mi)RNAs by high-throughput sequencing. Furthermore, we detected 150 differentially expressed mRNAs, 66 differentially expressed lncRNAs, and eight differentially expressed miRNAs. A functional enrichment analysis indicated that these genes are involved in multiple fat metabolism-related pathways, including positive regulation of fat cell differentiation, and fat digestion and absorption. We used various algorithms (miRanda, TargetScan, and RNAhybrid) to predict targeting relationships and constructed a competing endogenous RNA network containing seven lncRNAs, three miRNAs, and six mRNAs. All these genes were differentially expressed between the extremely high and low backfat thickness groups or enriched in pathways related to fat metabolism. Our results provide insight into the regulatory mechanisms by which non-coding RNAs and their target genes influence backfat deposition in pigs. Furthermore, our newly constructed competing endogenous RNA (lncRNA-miRNA-mRNA) network provides a basis for further exploration of fat deposition traits and non-coding RNA functions.

RNA sequencing analysis of the longissimus dorsi to identify candidate genes underlying the intramuscular fat content in Anqing Six-end-white pigs

Intramuscular fat (IMF) is a significant marker for pork quality. The Anqing Six-end-white pig has the characteristics of high meat quality and IMF content. Owing to the influence of European commercial pigs and a late start in resource conservation, the IMF content within local populations varies between individuals. This study analyzed the longissimus dorsi transcriptome of purebred Anqing Six-end-white pigs with varying IMF content to recognize differentially expressed genes. We identified 1528 differentially expressed genes between the pigs with high (H) and low (L) IMF content. Based on these data, 1775 Gene Ontology terms were significantly enriched, including lipid metabolism, modification and storage, and regulation of lipid biosynthesis. Pathway analysis revealed 79 significantly enriched pathways, including the Peroxisome proliferator-activated receptor and mitogen-activated protein kinase signaling pathways. Moreover, gene set enrichment analysis indicated that the L group had increased the expression of genes related to ribosome function. Additionally, the protein-protein interaction network analyses revealed that VEGFA, KDR, LEP, IRS1, IGF1R, FLT1 and FLT4 were promising candidate genes associated with the IMF content. Our study identified the candidate genes and pathways involved in IMF deposition and lipid metabolism and provides data for developing local pig germplasm resources.

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

BACKGROUND

Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes.

METHODS

We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence.

RESULTS

French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others).

CONCLUSIONS

These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.

Comprehensive analysis of miRNAs, lncRNAs and mRNAs profiles in backfat tissue between Daweizi and Yorkshire pigs

OBJECTIVE

Daweizi (DWZ) is a famous indigenous pig breed in China and characterized by tender meat and high fat percentage. However, the expression profiles and functions of transcripts in DWZ pigs is still in infancy. The object of this study was to depict the transcript profiles in DWZ pigs and screen the potential pathway influence adipogenesis and fat deposition.

METHODS

Histological analysis of backfat tissue was firstly performed between DWZ and lean-type Yorkshire pigs, and then RNA sequencing technology was utilized to explore miRNAs, lncRNAs and mRNAs profiles in backfat tissue. 18 differentially expressed (DE) transcripts were randomly selected for quantitative real-time polymerase chain reaction (QPCR) to validate the reliability of the sequencing results. Finally, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were conducted to investigate the potential pathways influence adipocyte differentiation, adipogenesis and lipid metabolism, and a schematic model was further proposed.

RESULTS

A total of 1,625 differentially expressed transcripts were identified in DWZ pigs, including 27 upregulated and 45 downregulated miRNAs, 64 upregulated and 119 downregulated lncRNA, 814 upregulated and 556 downregulated mRNAs. QPCR analysis exhibited strong consistency with the sequencing data. GO and KEGG analysis elucidated that the differentially expressed transcripts were mainly associated with cell growth and death, signal transduction, peroxisome proliferator-activated receptors (PPAR), AMP-activated protein kinase (AMPK), PI3K-Akt, adipocytokine and foxo signaling pathways, all of which are strongly involved in cell development, lipid metabolism and adipogenesis. Further analysis indicated that the BGIR9823_87926/miR-194a-5p/AQP7 network may be effective in the process of adipocyte differentiation or adipogenesis.

CONCLUSION

Our study provides comprehensive insights into the regulatory network of backfat deposition and lipid metabolism in pigs from the point of view of miRNAs, lncRNAs and mRNAs.

Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep

Background

During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments.

Methods

This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

Results

364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments.

Conclusions

This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.

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

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

A Comprehensive Analysis of the Myocardial Transcriptome in ZBED6-Knockout Bama Xiang Pigs

The ZBED6 gene is a transcription factor that regulates the expression of IGF2 and affects muscle growth and development. However, its effect on the growth and development of the heart is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) can regulate genes at the epigenetic, transcriptional, and posttranscriptional levels and play an important role in the development of eukaryotes. To investigate the function of ZBED6 in the cardiac development of pigs, we constructed the expression profiles of mRNAs and lncRNAs in myocardial tissue obtained from Bama Xiang pigs in the ZBED6 knockout group (ZBED6-KO) and the wild-type group (ZBED6-WT). A total of 248 differentially expressed genes (DEGs) and 209 differentially expressed lncRNAs (DELs) were detected, and 105 potential cis target genes of DELs were identified. The functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases revealed two GO items related to muscle development by the cis target genes of DELs. Moreover, IGF2 was the direct target gene of ZBED6 by ChIP-PCR experiment. Our results explored the mechanism and expression profile of mRNAs and lncRNAs of ZBED6 gene knockout on myocardium tissue development, mining the key candidate genes in that process like IGF2.

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.

Differential regulation of mRNAs and lncRNAs related to lipid metabolism in Duolang and Small Tail Han sheep

The function of long non-coding RNA (lncRNA) can be achieved through the regulation of target genes, and the deposition of fat is regulated by lncRNA. Fat has an important effect on meat quality. However, there are relatively few studies on lncRNAs in the subcutaneous adipose tissue of Duolang sheep and Small Tail Han sheep. In this study, RNA-Seq technology and bioinformatics methods were used to identify and analyze the lncRNA and mRNA in the subcutaneous adipose tissue of the two breeds of sheep. The results showed that 107 lnRNAs and 1329 mRNAs were differentially expressed. The differentially expressed genes and lncRNA target genes were significantly enriched in the biosynthesis of unsaturated fatty acids signaling pathway, fatty acid metabolism, adipocyte differentiation and other processes related to fat deposition. Among them, LOC105616076, LOC114118103, LOC105607837, LOC101116622, and LOC105603235 target FADS1, SCD, ELOVL6, HSD17B12 and HACD2, respectively. They play a key regulatory role in the biosynthesis of unsaturated fatty acids. This study lays a foundation for the study of the molecular mechanism of lncRNA on fat development, and has reference value for studying the differences in fat deposition between Duolang sheep and Small Tail Han sheep.

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.

Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis

The enzyme long-chain acyl-CoA synthetase 1 (ACSL1) is essential for lipid metabolism. The ACSL1 gene controls unsaturated fatty acid (UFA) synthesis as well as the formation of lipid droplets in bovine adipocytes. Here, we used RNA-Seq to determine lncRNA and mRNA that regulate UFA synthesis in bovine adipocytes using RNA interference and non-interference with ACSL1. The corresponding target genes of differentially expressed (DE) lncRNAs and the DE mRNAs were found to be enriched in lipid and FA metabolism-related pathways, according to GO and KEGG analyses. The differentially expressed lncRNA- differentially expressed mRNA (DEL-DEM) interaction network indicated that some DELs, such as TCONS_00069661, TCONS_00040771, TCONS_ 00035606, TCONS_00048301, TCONS_001309018, and TCONS_00122946, were critical for UFA synthesis. These findings assist our understanding of the regulation of UFA synthesis by lncRNAs and mRNAs in bovine adipocytes.

Identification and analysis of lncRNA, miRNA and mRNA related to subcutaneous and intramuscular fat in Laiwu pigs

BACKGROUND

Long non-coding RNAs (lncRNAs) regulate adipocyte differentiation and metabolism, However, their function on subcutaneous and intramuscular adipose tissues in pigs is unclear. Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), which severely affects the meat rate of pigs. It is of great significance for porcine breeding to study the mechanism of lncRNA related to adipogenesis and lipid metabolism.

METHODS

We identified differentially expressed lncRNAs, miRNAs and mRNAs in subcutaneous and intramuscular adipose tissues in three female Laiwu pigs by deep RNA-sequencing(|log2foldchange|≥1, P_value ≤ 0.05). The gene expression profiles of IMF and SCF in Laiwu pigs were comparatively analyzed by Bioinformatics methods to identify key lncRNAs, miRNAs, and mRNAs associated with lipid metabolism and adipogenesis.

RESULTS

A total of 1209 lncRNAs (DElncRNAs), 286 miRNAs (DEmiRNAs), and 1597 mRNAs (DEgenes) were differentially expressed between two types of adipose. Among them, 17 DElncRNAs and 103 target genes play a role in the co-expression network, as well as 59 DElncRNAs, 44 DEmiRNAs, and 88 DEgenes involved in ceRNA network. In GO(Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DElncRNAs their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as PPAR signaling pathway, Wnt signaling pathway, MAPK signaling pathway.

CONCLUSIONS

By constructing co-expression and ceRNAs network we found that Wnt signaling pathway play a critical regulatory role in intramuscular adipogenesis and lipid accumulation in Laiwu pigs. TCONS_00006525, TCONS_00046551 and TCONS_00000528 may target WNT5A, WNT10B and FDZ3 in co-expression network, TCONS_00026517 and other lncRNAs regulate the expression of PPARG, RXRG and SCD in ceRNA network, and were involved in Wnt signaling pathway. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation, predicting and treating diseases caused by ectopic fat.

Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.

LncRNA OIP5-AS1 Regulates the Warburg Effect Through miR-124-5p/IDH2/HIF-1α Pathway in Cervical Cancer

Hypoxia reprogrammed glucose metabolism affects the Warburg effect of tumor cells, but the mechanism is still unclear. Long-chain non-coding RNA (lncRNA) has been found by many studies to be involved in the Warburg effect of tumor cells under hypoxic condition. Herein, we find that lncRNA OIP5-AS1 is up-regulated in cervical cancer tissues and predicts poor 5-years overall survival in cervical cancer patients, and it promotes cell proliferation of cervical cancer cells in vitro and in vivo. Moreover, OIP5-AS1 is a hypoxia-responsive lncRNA and is essential for hypoxia-enhanced glycolysis which is IDH2 or hypoxia inducible factor-1α (HIF-1α) dependent. In cervical cancer cells, OIP5-AS1 promotes IDH2 expression by inhibiting miR-124-5p, and IDH2 promotes the Warburg effect of cervical under hypoxic condition through regulating HIF-1α expression. In conclusion, hypoxia induced OIP5-AS1 promotes the Warburg effect through miR-124-5p/IDH2/HIF-1α pathway in cervical cancer.

Comparison of long non-coding RNAs in adipose and muscle tissues between seven indigenous Chinese and the Yorkshire pig breeds

lncRNAs play crucial roles in fat metabolism in animals. Previously, we have compared the mRNA transcriptome profiles between seven fat-type Chinese pig breeds and one lean-type Western breed (Yorkshire, YY). The associations between differentially expressed (DE) genes and phenotypical traits were investigated. In the present study, to further explore the underlying regulatory mechanisms, lncRNAs were sequenced and compared between YY and Chinese indigenous breeds. The results showed 9114 and 7538 DE lncRNAs between at least one Chinese breed and the YY breed in the adipose and muscle tissue respectively. KEGG enrichment analysis revealed that the target genes of these DE lncRNAs mainly influenced the glucolipid metabolism, which is an important process affecting meat quality. Correlation analyses between the DE lncRNA and DE mRNA genes related to meat quality and growth traits were performed. The results showed that LTCONS_00073280 was associated with intramuscular fat content. Four lncRNAs (LTCONS_00101781, LTCONS_00037879, LTCONS_00088260 and LTCONS-00128343) might mediate backfat thickness. Overall, this study provides candidate lncRNAs that potentially affect meat quality, which might be useful for molecular breeding of pig breeds in future.

Single-nucleotide polymorphism detecting of some candidate genes related to lipid metabolism in Booroola Merino-Afshari sheep by Bayesian model averaging

This study was designed to identify single-nucleotide polymorphisms (SNPs) of some candidate genes related to lipid metabolism and their association with carcass fat in male crossbred lambs. Hence, 96 of almost 11-month-old Booroola Merino-Afshari crossbred lambs (first-generation backcross) were used by considering their phenotypic carcass traits. Then, DNA was extracted and DNA targets were amplified using designed specific primers by PCR procedure. Identification of potential SNPs was done by a direct sequencing method for LEP, FABP4, DGAT1, GH, and TRIB3 genes using the sequencing-RFLP procedure. Then, the most probable statistical models based on additive and genotypic effects of identified SNPs in each trait were obtained by the Bayesian model averaging (BMA) approach of R software (Ver. 3.3.1) to assess the association of SNPs with traits. Detected SNPs in this study included two SNPs in exon 3 of LEP, one SNP in exon 2 of TRIB3, one SNP in intron 2 of FABP4, one SNP in 5' UTR of DGAT1, and two SNPs in 3' UTR of GH genes. For carcass weight trait, one of the identified SNP genotypes in the LEP (c.587G > A) had a higher probability in the model. Carcass weight of lambs with GA genotype was 2.46 kg heavier than GG genotype. Also, two genes of TRIB3 and GH2 had the highest probability in the models of fat tail and waste weight, respectively. Based on the results, these polymorphisms can be used in the marker-assisted selection of breeding programs and designing DNA chips for genomic selection.

IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition

Background

Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF.

Results

A total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (< 10 kb) in pig and humans. Real-time quantitative polymerase chain reaction (RT-qPCR) validation study indicated that nuclear receptor subfamily 4 group A member 3 (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3.

Conclusions

In conclusion, a novel functional noncoding variation named IRLnc has been found contribute to IMF by regulating the expression of NR4A3. These findings suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07349-5.

Profiling of skeletal muscle tissue for long non-coding RNAs related to muscle metabolism in the QingYu pig at the growth inflection point

OBJECTIVE

Investigation of muscle growth at different developmental stages is an appropriate strategy for studying the mechanisms underlying muscle development and differences in phenotypes. In particular, the muscle development mechanisms and the difference between the fastest and slowest growth rates.

METHODS

In this study, we used a growth curve model to fit the growth inflection point (IP) of QingYu pigs and compared differences in the long non-coding RNA (lncRNA) transcriptome of muscle both at the growth IP and plateau phase (PP).

RESULTS

The growth curve of the QingYu pig had a good fit (R2 = 0.974) relative to a typical S-curve and reached the IP at day 177.96. At the PP, marbling, intramuscular fat, and monounsaturated fatty acids had increased significantly and the percentage of lean muscle and polyunsaturated fatty acids had decreased. A total of 1,199 mRNAs and 62 lncRNAs were differentially expressed at the IP compared with the PP. Additional to gene ontology and Kyoto encyclopedia of genes and genomes pathway analyses, these differentially expressed protein coding genes were principally related to muscle growth and lipid metabolism.

CONCLUSION

Our results suggest that the identified differentially expressed lncRNAs, could play roles in muscle growth, fat deposition and regulation of fatty acid composition at the IP and PP.

Identification of genes related to intramuscular fat independent of backfat thickness in Duroc pigs using single-step genome-wide association

Intramuscular fat (IMF) is an important meat-quality trait of pigs, which influences pork's shearing force, hydraulics, tenderness and juicy flavor. However, to achieve a higher percentage of lean meat, pigs with lower backfat thickness (BF) are intensively selected for, which may lead to a reduction in pork quality. Therefore, the objective of this study was to locate loci that affect IMF without changing BF. A single-step GWAS was performed on 950 Duroc pigs genotyped by a 50K SNP chip in order to detect genomic variants relevant to IMF and BF. The significant SNPs detected were afterwards divided into a BF subset (seven SNPs), an IMF subset (11 SNPs) and a subset of both traits (12 SNPs), according to their P-value and LD. After SNP and QTL annotation, our results indicated that SSC1: 167938652, 166363826, 164829874 and 167171587 might be associated with IMF without changing BF. In the subset of both traits, we found that the combined effect of ALGA0006602 (SSC1: 159538854) and 12784636 (SSC1: 160773437) might improve the IMF without changing BF. Our gene annotation result showed that TLE3, ITGA11, SMAD6, PAQR5 and [RNF152^A/G × MC4R^A/A ] genes might affect IMF independently of BF. We believe that the SNPs and genes identified in this study will be valuable for the future molecular breeding of IMF in Duroc pigs.

Long non-coding RNA CDKN2B-AS1 contributes to atherosclerotic plaque formation by forming RNA-DNA triplex in the CDKN2B promoter

BACKGROUND

Atherosclerosis involves a slow process of plaque formation on the walls of arteries, and comprises a leading cause of cardiovascular disease. Long non-coding RNAs (lncRNAs) have been implicated in the pathogenesis of atherosclerosis. In this study, we aim to explore the possible involvement of lncRNA 'cyclin-dependent kinase inhibitor 2B antisense noncoding RNA' (CDKN2B-AS1) and CDKN2B in the progression of atherosclerosis.

METHODS

Initially, we quantified the expression of CDKN2B-AS1 in atherosclerotic plaque tissues and, in THP-1 macrophage-derived, and human primary macrophage (HPM)-derived foam cells. Next, we established a mouse model of atherosclerosis using apolipoprotein E knockout (ApoE-/-) mice, where lipid uptake, lipid accumulation, and macrophage reverse cholesterol transport (mRCT) were assessed, in order to explore the contributory role of CDKN2B-AS1 to the progression of atherosclerosis. RIP and ChIP assays were used to identify interactions between CDKN2B-AS1, CCCTC-binding factor (CTCF), enhancer of zeste homologue 2 (EZH2), and CDKN2B. Triplex formation was determined by RNA-DNA pull-down and capture assay as well as EMSA experiment.

FINDINGS

CDKN2B-AS1 showed high expression levels in atherosclerosis, whereas CDKN2B showed low expression levels. CDKN2B-AS1 accelerated lipid uptake and intracellular lipid accumulation whilst attenuating mRCT in THP-1 macrophage-derived foam cells, HPM-derived foam cells, and in the mouse model. EZH2 and CTCF were found to bind to the CDKN2B promoter region. An RNA-DNA triplex formed by CDKN2B-AS1 and CDKN2B promoter was found to recruit EZH2 and CTCF in the CDKN2B promoter region and consequently inhibit CDKN2B transcription by accelerating histone methylation.

INTERPRETATION

The results demonstrated that CDKN2B-AS1 promotes atherosclerotic plaque formation and inhibits mRCT in atherosclerosis by regulating CDKN2B promoter, and thereby could be a potential therapeutic target for atherosclerosis.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (F_ROH>4Mb = 0.400 and F_ROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (F_ROH>4Mb = 0.098 and F_ROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.

Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review

Modern pig breeds, which have been genetically improved to achieve fast growth and a lean meat deposition, differ from local pig breeds with respect to fat deposition, fat specific metabolic characteristics and various other properties. The present review aimed to elucidate the mechanisms underlying the differences between fatty local and modern lean pig breeds in adipose tissue deposition and lipid metabolism, taking into consideration morphological, cellular, biochemical, transcriptomic and proteomic perspectives. Compared to modern breeds, local pig breeds accumulate larger amounts of fat, which generally contains more monounsaturated and saturated fatty acids; they exhibit a higher adipocyte size and higher activity of lipogenic enzymes. Studies using transcriptomic and proteomic approaches highlighted several processes like immune response, fatty-acid turn-over, oxidoreductase activity, mitochondrial function, etc. which differ between local and modern pig breeds.

Molecular cloning of SLC35D3 and analysis of its role during porcine intramuscular preadipocyte differentiation

Background

Solute carrier family 35 (SLC35) is one of a large number of membrane transporter protein families. Member D3 of this family is thought to be involved in adipose deposition and metabolic control.

Results

We obtained 2238 bp cDNA of porcine SLC35D3, it contains a 1272 bp ORF, encoding a 423 amino acid polypeptide, and a 966 bp 3′ UTR. BLAST results revealed that the amino acid sequence of porcine SLC35D3 had the closest phylogenetic relationship with members of the genus Ovis aries. Further bioinformatics analysis showed that the SLC35D3 protein contains 8 transmembrane domains, and that there is no signal peptide structure. The secondary structure of the protein mainly contains 37.12% α-helixes, 7.8% in β-folds, and 33.57% random coils. mRNA expression analysis showed that SLC35D3 is expressed in lung, liver, heart, spleen, kidney, longissimus dorsi muscle (LDM), leaf fat (LF), and subcutaneous adipose tissue (SAT). To examine the effects of SLC35D3 expression on fat synthesis and catabolism, SLC35D3-siRNA was transfected into cultured intramuscular adipocytes. SLC35D3 silenced cells showed increased expression of genes related to fat synthesis, and increased deposition of intramuscular fat (IMF), abundance of lipid droplets, and the level of free fatty acid (FFA) in the culture medium. In contrast, the siRNA decreased the expression genes involved in fat catabolism.

Conclusions

Our results demonstrate that silenced SLC35D3 results in increased adipogenic processes in pig intramuscular adipocytes. These data represent the first exploration of SLC35D3 expression in swine, and provide valuable insights into the functions of SLC35D3 in adipocyte differentiation.

Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species

BACKGROUND

Lipids are important for the cell and organism life since they are major components of membranes, energy reserves and are also signal molecules. The main organs for the energy synthesis and storage are the liver and adipose tissue, both in humans and in more distant species such as chicken. Long noncoding RNAs (lncRNAs) are known to be involved in many biological processes including lipid metabolism.

RESULTS

In this context, this paper provides the most exhaustive list of lncRNAs involved in lipid metabolism with 60 genes identified after an in-depth analysis of the bibliography, while all "review" type articles list a total of 27 genes. These 60 lncRNAs are mainly described in human or mice and only a few of them have a precise described mode-of-action. Because these genes are still named in a non-standard way making such a study tedious, we propose a standard name for this list according to the rules dictated by the HUGO consortium. Moreover, we identified about 10% of lncRNAs which are conserved between mammals and chicken and 2% between mammals and fishes. Finally, we demonstrated that two lncRNA were wrongly considered as lncRNAs in the literature since they are 3' extensions of the closest coding gene.

CONCLUSIONS

Such a lncRNAs catalogue can participate to the understanding of the lipid metabolism regulators; it can be useful to better understand the genetic regulation of some human diseases (obesity, hepatic steatosis) or traits of economic interest in livestock species (meat quality, carcass composition). We have no doubt that this first set will be rapidly enriched in coming years.

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12

Sequencing technology, especially next-generation RNA sequencing, has greatly facilitated the identification and annotation of long noncoding RNAs (lncRNAs). In mammals, a large number of lncRNAs have been identified, which regulate various biological processes. An increasing number of lncRNAs have been identified which could function as key regulators of adipogenesis (adipocyte formation), a key step of the development of adipose tissue. Because proper adipose tissue development is a key factor affecting animal growth efficiency, lean/fat ratio, and meat quality, summarizing the roles and recent advances of lncRNAs in adipogenesis is needed in order to develop strategies to effectively manage fat deposition. In this review, we updated lncRNAs contributed to the regulation of adipogenesis, focusing on their roles in fat development of farm animals.

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.

Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs

Adipose deposits influence the quality of ruminant carcasses, and in suckling lambs, internal types of adipose deposits represent a notable proportion of total fat. The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf, n = 8; Churra, n = 6) was used for the RNA-seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The expression of the UCP1 gene, a classical biomarker of brown fat, and the presence of multilocular adipocytes in the two breeds supported the presence of brown fat at the transition stage towards white fat tissue. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. Brown/white fat gene biomarkers were not included in the list of DEGs. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, whereas in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, whereas the Churra upregulated DEGs are linked to fat accumulation. These results can help to increase knowledge of the genes controlling early fat deposition in ruminants and shed light on fundamental aspects of adipose tissue growth.

Transcriptome Analysis of Adipose Tissue Indicates That the cAMP Signaling Pathway Affects the Feed Efficiency of Pigs

Feed efficiency (FE) is one of the main factors that determine the production costs in the pig industry. In this study, RNA Sequencing (RNA-seq) was applied to identify genes and long intergenic non-coding RNAs (lincRNAs) that are differentially expressed (DE) in the adipose tissues of Yorkshire pigs with extremely high and low FE. In total, 147 annotated genes and 18 lincRNAs were identified as DE between high- and low-FE pigs. Seventeen DE lincRNAs were significantly correlated with 112 DE annotated genes at the transcriptional level. Gene ontology (GO) analysis revealed that DE genes were significantly associated with cyclic adenosine monophosphate (cAMP) metabolic process and Ca²⁺ binding. cAMP, a second messenger has an important role in lipolysis, and its expression is influenced by Ca²⁺ levels. In high-FE pigs, nine DE genes with Ca²⁺ binding function, were down-regulated, whereas S100G, which encodes calbindin D9K that serve as a Ca²⁺ bumper, was up-regulated. Furthermore, ATP2B2, ATP1A4, and VIPR2, which participate in the cAMP signaling pathway, were down-regulated in the upstream of lipolysis pathways. In high-FE pigs, the key genes involved in the lipid biosynthetic process (ELOVL7 and B4GALT6), fatty acid oxidation (ABCD2 and NR4A3), and lipid homeostasis (C1QTNF3 and ABCB4) were down-regulated. These results suggested that cAMP was involved in the regulation on FE of pigs by affecting lipid metabolism in adipose tissues.