Fat Deposition In Sheep Research Articles

Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study

Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study

Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies.

The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration. A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails. The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep. The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.

Potential of different strategies to increase intramuscular fat deposition in sheep: A meta-analysis study

We evaluated the potential of different strategies to increase intramuscular fat (IMF) deposition in sheep meat through meta-analytical methods. Additionally, this study aimed to investigate the interrelationship among diet composition, performance, carcass traits, meat quality, marbling score and IMF in sheep. The dataset was composed by 102 peer-reviewed publications. The strategies to increase IMF deposition in sheep meat were evaluated by examining the weighted mean difference (WMD) between control treatment and increased-IMF treatment (beta-agonist; glycerin; essential oil; vitamin E; lipids; tannins; feeding system and sex class). The interplay between factors such as dietary composition, performance, carcass and meat quality traits highlights how the intensification of production systems, characterized by a high grain content in the diet and shorter finishing periods, reduces IMF content of meat. The IMF content was greater in females (WMD = 0.52%; P<.0001) and castrated males (WMD = 0.53%; P = 0.001) compared to intact males. Lambs finished in feedlots exhibited a 19.23% higher IMF content (WMD = 0.74%; P <.0001) compared to those finished in pasture systems. The inclusion of lipids sources to the diets increased in IMF content (WMD = 0.11%; P = 0.008), while tannins sources decrease in IMF (WMD = −0.07%; P = 0.029). Marbling score did not prove to be an adequate indicator of IMF deposition in sheep meat, potentially due to biases in subjective marbling assessments. In conclusion, our findings suggest that the most effective strategy for enhancing IMF in lambs involves utilizing female or castrated males rather than intact males followed by finishing lambs on high concentrate diets in a feedlot. Genetics did not impact IMF in the evaluated studies while other dietary strategies to alter IMF deposition had mixed effects on IMF deposition. Tannin marginally decreased IMF, vitamin E had no effect, and lipid supplementation had varied effects on IMF deposition depending on the lipid source.

Screening and identification of lncRNAs in preadipocyte differentiation in sheep

Studies of preadipocyte differentiation and fat deposition in sheep have mainly focused on functional genes, and with no emphasis placed on the role that long non-coding RNAs (lncRNAs) may have on the activity of those genes. Here, the expression profile of lncRNAs in ovine preadipocyte differentiation was investigated and the differentially expressed lncRNAs were screened on day 0 (D0), day 2(D2) and day 8(D8) of ovine preadipocyte differentiation, with their target genes being predicted. The competing endogenous RNA (ceRNA) regulatory network was constructed by GO and KEGG enrichment analysis for functional annotation, and some differentially expressed lncRNAs were randomly selected to verify the RNA-Seq results by RT-qPCR. In the study, a total of 2517 novel lncRNAs and 3943 known lncRNAs were identified from ovine preadipocytes at the three stages of differentiation, with the highest proportion being intergenic lncRNAs. A total of 3455 lncRNAs were expressed at all three stages of preadipocyte differentiation, while 214, 226 and 228 lncRNAs were uniquely expressed at day 0, day 2 and day 8, respectively. By comparing the expression of the lncRNAs between the three stages of differentiation stages, a total of 405, 272 and 359 differentially expressed lncRNAs were found in D0-vs-D2, D0-vs-D8, and D2-vs-D8, respectively. Functional analysis revealed that the differentially expressed lncRNAs were enriched in signaling pathways related to ovine preadipocyte differentiation, such as mitogen-activated protein kinase (MAPK) pathway, the phosphoinositide 3-kinase protein kinase B (PI3K-Akt) pathway, and the transforming growth factor beta (TGF-β) pathway. In summary, lncRNAs from preadipocytes at different stages of differentiation in sheep were identified and screened using RNA-Seq technology, and the regulatory mechanisms of lncRNAs in preadipocyte differentiation and lipid deposition were explored. This study provides a theoretical reference for revealing the roles of lncRNAs in ovine preadipocyte differentiation and also offers a theoretical basis for further understanding the regulatory mechanisms of ovine preadipocyte differentiation.

The Effects of DDI1 on Inducing Differentiation in Ovine Preadipocytes via Oar-miR-432.

Reducing fat deposition in sheep (Ovis aries) tails is one of the most important ways to combat rising costs and control consumer preference. Our previous studies have shown that oar-miR-432 is differentially expressed in the tail adipose tissue of Hu (a fat-tailed sheep breed) and Tibetan (a thin-tailed sheep breed) sheep and is a key factor in the negative regulation of fat deposition through BMP2 in ovine preadipocytes. This study investigated the effect of oar-miR-432 and its target genes in ovine preadipocytes. A dual luciferase assay revealed that DDI1 is a direct target gene of oar-miR-432. We transfected an oar-miR-432 mimic and inhibitor into preadipocytes to analyze the expression of target genes. Overexpression of oar-miR-432 inhibits DDI1 expression, whereas inhibition showed the opposite results. Compared with thin-tailed sheep, DDI1 was highly expressed in the fat-tailed sheep at the mRNA and protein levels. Furthermore, we transfected the overexpression and knockdown target genes into preadipocytes to analyze their influence after inducing differentiation. Knockdown of DDI1 induced ovine preadipocyte differentiation into adipocytes but suppressed oar-miR-432 expression. Conversely, the overexpression of DDI1 significantly inhibited differentiation but promoted oar-miR-432 expression. DDI1 overexpression also decreased the content of triglycerides. Additionally, DDI1 is a nested gene in intron 1 of PDGFD. When DDI1 was overexpressed, the PDGFD expression also increased, whereas DDI1 knockdown showed the opposite results. This is the first study to reveal the biological mechanisms by which oar-miR-432 inhibits preadipocytes through DDI1 and provides insight into the molecular regulatory mechanisms of DDI1 in ovine preadipocytes. These results have important applications in animal breeding and obesity-related human diseases.

The role of miR-369-3p in proliferation and differentiation of preadipocytes in Aohan fine-wool sheep.

MicroRNAs (miRNAs) are a large class of non-coding RNAs that play important roles in the proliferation and differentiation of adipocytes. Our previous sequencing analysis revealed higher expression of miR-369-3p in the longissimus muscle of 2-month-old Aohan fine-wool sheep (AFWS) compared to 12-month-old sheep (), suggesting that miR-369-3p may regulate fat deposition in AFWS. To test this, miR-369-3p mimics, inhibitors, and negative controls (NCs) were constructed and transfected into AFWS preadipocytes. After transfection with miR-369-3p mimics, we found a decrease () in the expression of genes and proteins related to cell proliferation and differentiation, detected by RT-qPCR (quantitative reverse transcription PCR) and western blot analyses. Moreover, EdU (5-ethynyl-2-deoxyuridine) detection and Oil Red O staining showed a decrease () in cell proliferation and lipid accumulation, respectively. The opposite trends () were obtained after transfection with miR-369-3p inhibitors. In conclusion, the results showed that miR-369-3p can inhibit the proliferation and differentiation of AFWS preadipocytes, providing a theoretical basis to further explore the molecular mechanism of fat deposition in sheep and other domestic animals.

Copy number variation association studies for sheep tail-relevant traits in Hulunbuir sheep.

Tail type is an important trait that influences meat quality and consumer purchasing attitudes. As a novel genetic marker, the study of genomic copy number variations (CNVs) provides a new research method to study the genetic mechanisms underlying trait formation. In the present paper, we conducted CNV-based association studies for sheep tail type and growth traits in Hulunbuir sheep. A total of 167 CNVs and 288 individuals were analyzed at the marker and individual level, respectively. Association studies of 10 traits were carried out using two mixed linear models. We found that three, one and one CNV loci were significantly associated with tail type, tail length and tail fat weight, respectively, which together contained a total of 52 candidate genes. Out of these genes, five have been documented to be associated with fat metabolism in sheep. Our findings provide a reference for further studies on fat deposition in sheep as well as a theoretical basis for breeding Hulunbuir sheep with the required tail type.

Ovine RAP1GAP and rBAT gene polymorphisms and their association with tail fat deposition in Hu sheep.

Excessive fat deposition in the tail of sheep will affect its feed efficiency, which will increase the feeding cost. The purpose of this study was to identify the single nucleotide polymorphisms (SNPs) of RAP1GAP and rBAT genes by PCR amplification and Sanger sequencing, the SNPs were genotyped by KASP genotyping assays to evaluate their association with tail fat deposition traits. The results showed that two intronic mutations of g.13561 G > A and g.1460 T > C were found in RAP1GAP and rBAT, respectively. There were three genotypes of GG, AG, AA and CC, CT and TT at these two loci, respectively. Association analysis showed that g.13561 G > A of RAP1GAP was associated with tail width, tail fat weight and relative tail fat weight (P < 0.05). The g.1460 T > C of rBAT was associated with tail width and tail fat weight (P < 0.05). Different combinations of genotypes also differed significantly with tail fat deposition traits. In the tail fat tissue, the expression levels of RAP1GAP gene was significantly higher in small-tailed sheep than in big-tailed sheep, and the expression levels of rBAT gene was significantly higher in big-tailed sheep than in small-tailed sheep. In the liver, the expression levels of RAP1GAP and rBAT gene was significantly higher at 6 months than at 0 and 3 months. In conclusion, RAP1GAP and rBAT polymorphisms can be used as a candidate molecular marker to reduce tail fat deposition in sheep.

Distribution and Difference of Gastrointestinal Flora in Sheep with Different Body Mass Index.

Simple SummaryFat deposition capacity greatly impacts the production capacity of sheep. The production of high amounts of fat affects the economic benefits of animals. Gastrointestinal microorganisms play an important role in the characteristics of host fat deposition. This study compares differences in gastrointestinal microorganisms in sheep with different body mass indices. Results showed that there were different microflora compositions among different groups. This provides a new idea for the regulation of fat deposition traits in sheep.Fat deposition is the key factor affecting the efficiency of animal husbandry production. There are many factors affecting fat deposition, in which the gastrointestinal microbiota plays an important role. Therefore, the body mass index (BMI) was introduced into the evaluation of sheep fat deposition, and the different microbiota and functional pathways of the sheep gastrointestinal tract in different BMI groups were analyzed. We selected 5% of individuals with the highest and lowest BMI from a feed test population (357 in whole group). Microorganisms in 10 sites of the gastrointestinal tract in 36 individuals (18 in each group) were evaluated by 16S rRNA V3–V4 region sequencing. There were differences (p < 0.05) in fat deposition traits between different BMI groups. In the 10 parts of the gastrointestinal tract, the diversity and richness of cecal microflora in the high-BMI group were higher than those in low-BMI Hu sheep (p < 0.05). Principal coordinate analysis (PCoA) showed that there was separation of the cecum between groups, and there were differences in the cecal microbial community. Linear discriminant analysis effect size (LEfSe) showed that most biomarkers were in the cecum. On the basis of an indepth study of cecal microorganisms, 26 different bacterial genera were obtained (p < 0.05). Correlation analysis between them and the characteristics of fat deposition in sheep showed that Colidextribacter, Alloprevotella, and Succenivibrio were positively correlated with fat deposition, while Lachnospiraceae_ND3007_Group was negatively correlated (p < 0.05). The above results show that the cecum may be an important part leading to the difference of BMI in sheep, and its microorganisms may affect the level of fat deposition.

Genetic polymorphisms within the ETAA1 gene associated with growth traits in Chinese sheep breeds.

Ewing tumor-associated antigen 1 (ETAA1) is an important candidate gene for fat deposition in sheep. This study aimed to investigate the indel variations in the ETAA1gene and their associations with growth traits in the 1619sheep. The polymorphism information content of this indel ranged from 0.308 to 0.375, with medium genetic diversity (0.25 ≤ polymorphism information content ≤ 0.5). The correlation analysis showed that an 8-bp insertion within the ETAA1gene was significantly associated with growth traits in Luxi Blackhead sheep (LXBH), Lanzhou fat-tailed sheep, Hu sheep, Tong sheep, and Tan sheep (p<0.05). Furthermore, the ETAA1gene was significantly associated with several growth traits (p<0.01), such as chest width and paunch girth of LXBH, Tong, and Tan rams. It was significantly related to the body morphometric traits of LXBH, Lanzhou fat-tailed sheep, Hu, Tong, and Tan ewes. In conclusion, the detected 8-bp indel within the ETAA1gene was confirmed in sheep, significantly affecting the growth traits, and might be a potential DNA marker for the selection of high-quality individuals in marker-assisted selection for sheep breeding.

Ovine ELOVL5 and FASN genes polymorphisms and their correlations with sheep tail fat deposition.

Reducing tail fat deposition can increase the economic value of a carcass and improve feed efficiency. This study aimed to explore ELOVL5 and FASN polymorphisms associated with tail fat deposition and their expression levels of sheep. Association analysis showed that ELOVL5 synonymous mutation g.62534 C>T was associated with tail width, tail fat weight, and relative tail fat weight (P<0.05). FASN synonymous mutation g.12694 A>G was associated with tail length and width (P<0.05). Combined effect analyses indicated significant differences between the combined genotypes and tail fat deposition. Quantitative real-time reverse transcription PCR indicated that the ELOVL5 and FASN expression levels were significantly higher in tail fat than in other tissues (P<0.05). ELOVL5 expression levels in tail-fat tissue of big-tail sheep was significantly higher than that in small-tail sheep (P<0.01). FASN expression levels were significantly higher in tail-fat tissue of small-tail sheep than in that of big-tail sheep (P<0.05). During development, ELOVL5 tail fat expression increased significantly from 0 to 6months old (P<0.05), and FASN expression at 3months old was significantly higher than that at 0 (minimum) and 6months old (P<0.05). Therefore, ELOVL5 and FASN polymorphisms could represent new candidate molecular markers and targets to reduce tail fat deposition in sheep.

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat.

BackgroundNowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear.MethodsIn the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs.ResultsIn the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

Effect of the ACAA1 Gene on Preadipocyte Differentiation in Sheep.

Acetyl-CoA acyltransferase 1 (ACAA1) functions as a key regulator of fatty acid β-oxidation in peroxisomes by catalyzing the cleavage of 3-ketoacyl-CoA to acetyl-CoA and acyl-CoA, which participate in the extension and degradation of fatty acids. Thus, ACAA1 is an important regulator of lipid metabolism and plays an essential role in fatty acid oxidation and lipid metabolism. Our previous study findings revealed that ACAA1 is closely associated with the peroxisome proliferator-activated receptor (PPAR) signaling and fatty acid metabolism pathways, which are involved in fat deposition in sheep, leading to our hypothesis that ACAA1 may be involved in fat deposition by regulating lipid metabolism. However, the associated molecular mechanism remains unclear. In the present study, to assess the potential function of ACAA1 in sheep preadipocyte differentiation, we knocked down and overexpressed ACAA1 in sheep preadipocytes and evaluated the pattern of ACAA1 gene expression during preadipocyte differentiation by qRT-PCR. ACAA1 was significantly expressed in the early stage of adipocyte differentiation, and then its expression decreased. ACAA1 deficiency increased lipid accumulation and the triglyceride content and promoted sheep preadipocyte differentiation, whereas ACAA1 overexpression inhibited adipogenesis and decreased lipid accumulation and the triglyceride content. Simultaneously, we demonstrated that ACAA1 deficiency upregulated the expressions of the adipogenic marker genes PPARγ and C/EBPα in sheep preadipocytes, but ACAA1 overexpression inhibited the expressions of these markers, indicating that ACAA1 affects lipid metabolism by regulating adipogenic marker genes. Our results may promote a better understanding of the regulation of adipogenesis by ACAA1.

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

BackgroundIntramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China’s most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12).ResultsWe identified a total of 26,247 genes and 6935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.ConclusionsOur study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.

Transcriptomic analyses revealed common tailed and perirenal adipose differentially expressed genes in four Chinese indigenous sheep breeds

ABSTRACT Fat deposition and distribution in different body sites are associated with livestock productivity. In some sheep breeds, fat is excessively accumulated around the tail region, which is regarded as the fat-tail phenotype. Though some plausible genes or genomic regions associated with the fat-tail phenotype were identified, further validation of them in different individuals and breeds is still required. In this study, we implemented differential expression analysis using RNA-seq data in longissimus dorsi muscle tissue (MUT), perirenal adipose tissue (PAT) and tail adipose tissue (TAT) of Hu sheep, which is a representative of short fat-tailed sheep. The result identified 1336, 427 and 665 differentially expressed genes (DEGs) in MUT, PAT and TAT of Hu sheep respectively. Of those, 600 DEGs and 336 DEGs showed unique expression in TAT and PAT, respectively. In addition, integrated analyses of our data with published data from small-tailed Han sheep, Guangling large-tailed sheep and Tan sheep found 9 DEGs in PAT and 13 DEGs in TAT of Hu sheep have similar expression patterns in the remaining three sheep breeds. Among 9 DEGs in PAT, WT1, TCF21, PPFIBP1 and WNT10B may have important roles in perirenal adipose formation. Among 13 DEGs in TAT, PKD2L1 and MST1 may play significant roles in the maintenance of unsaturated fatty acid content in TAT. Five genes that were previously reported to be correlated with tailed fat deposition were further validated in current study, including CITED1, HOTAIR_2, HOTAIR_3, HOXC12 and HOXC13. Furthermore, we also investigated the expression pattern of 42 candidate genes identified by selection signature analysis or genome wide association analysis from published studies. Two of them were found to be highly expressed in TAT, including PPP1CA and PEX6. Our findings identify candidate genes for tail fat deposition across different breeds and pave a solid foundation for studying the regulation of fat deposition in sheep in the future.

MicroRNA expression patterns in tail fat of different breeds of sheep

Abstract The objective of this study was to detect the expression profile of microRNAs (miRNAs) in two breeds of fat-tailed sheep (Guangling Large-tailed sheep and Small-tailed Han sheep), and discover the miRNAs that may play roles in lipid metabolism. Consequently, two small RNA libraries were constructed and high-throughput sequencing was used to identify the miRNAs expressed in the two libraries and to calculate the expression of miRNAs. Bioinformatics methods were used to predict target genes, which were subsequently analyzed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). Nine miRNAs (miR-10b, miR-29a, miR-30c, miR-155, miR-192, miR-206, novel-miR-102, novel-miR-36, and novel-miR-63) were chosen to verify the sequencing results by detecting their expressions in the two breeds using quantitative real-time PCR. A total of 113 and 131 conserved miRNAs in the two breeds were obtained, of which 40 miRNAs were differentially expressed. KEGG analysis showed that many predicted target genes for these miRNAs are involved in lipid metabolism pathways. By screening the unknown miRNAs using MIREAP, 208 and 215 novel miRNAs were obtained from the two libraries, of which 150 were significantly different. This study represents the comprehensive survey of miRNAs expressed in the tail fat of two breeds of sheep with different tail fat deposition using HiSeq analysis. We conclude that differentially expressed miRNAs may play roles in regulating adipose metabolism, and thus, may contribute to improving the meat quality and fat deposition in sheep.

Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep.

MicroRNAs (miRNAs) are endogenous, noncoding RNAs that regulate various biological processes including adipogenesis and fat metabolism. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs involved in fat deposition in adipose tissues from fat-tailed (Kazakhstan sheep, KS) and thin-tailed (Tibetan sheep, TS) sheep breeds. By comparing HiSeq data of these two breeds, 539 miRNAs were shared in both breeds, whereas 179 and 97 miRNAs were uniquely expressed in KS and TS, respectively. We also identified 35 miRNAs that are considered to be putative novel miRNAs. The integration of miRNA-mRNA analysis revealed that miRNA-associated targets were mainly involved in the gene ontology (GO) biological processes concerning cellular process and metabolic process, and miRNAs play critical roles in fat deposition through their ability to regulate fundamental pathways. These pathways included the MAPK signaling pathway, FoxO and Wnt signaling pathway, and focal adhesion. Taken together, our results define miRNA expression signatures that may contribute to fat deposition and lipid metabolism in sheep.

Signatures of selection identify loci associated with fat tail in sheep.

Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging applications of dense marker panels in animal genetics. In this study, a genomewide scan using approximately 50,000 SNP was performed in an attempt to identify genomic regions associated with fat deposition in sheep, the importance of this not only being limited to livestock facing future climate changes but also for elucidating the physiology of lipid metabolism. The genotyping results obtained with the Ovine SNP50K BeadChip in 2 fat tail breeds were compared with those obtained in 13 thin tail breeds. Direct sequencing of the annotated genes located in proximity to the markers with opposite allele frequency in thin tail vs. fat tail sheep gave additional SNP of interest. To further confirm the results of the genomewide scan, we genotyped the SNP within these genes in the 2 groups of sheep. A missense mutation in the gene, with different allele frequency in the 2 groups, was detected. The results indicated and as the most probable genes involved in the fat tail phenotype.

Allelic variation in ovine fatty acid-binding protein (FABP4) gene

The fatty acid-binding protein 4 (FABP4) plays a role in lipid metabolism and has been implicated in intra-cellular lipid transport. While FABP4 variation has been reported in some species, variation in the coding sequence has not been reported in sheep. In this study two regions of ovine FABP4 were analysed using PCR-SSCP and sequencing. Five different PCR-SSCP patterns, representing five specific sequences (A ( 1 )-E ( 1 )) were detected in region 1 (exon 2-intron 2) with sequence analysis revealing three nucleotide substitutions and one deletion in the intron. In region 2 (exon 3-intron 3), four different PCR-SSCP patterns (A ( 2 )-D ( 2 )) were observed and four nucleotide substitutions were revealed. In total, fourteen haplotypes through both regions were defined. There was a difference (P < 0.001) in allele frequencies between two selection lines of Coopworth sheep that have been bred over many generations to be lean or fat. In region 1, A ( 1 ) and B ( 1 ) were most common (at a frequency of 50 and 30 % respectively) in the fat line, whereas these two variants were absent or rare in the lean line in which C ( 1 ) predominated (89 %). In region 2, C ( 2 ) was the most common variant (59 %) in the lean line but was absent in the fat line, whereas B ( 2 ) was predominant (83 %) in the fat line but was rare (3 %) in the lean line. These results indicate that ovine FABP4 is polymorphic and suggest further analysis is required to see if the variation detected affects fat deposition in sheep.