A missense mutant of the PPAR-γ gene associated with carcass and meat quality traits in Chinese cattle breeds

Expression profile of FASN gene and association of its polymorphisms with intramuscular fat content in Hu sheep

The content of intramuscular fat (IMF) is one of the most important factors that has a large impact on meat quality, and it is an effective way to improve IMF according to marker-assisted selection (MAS). Fatty-acid synthase (FASN) is a key gene in meat lipid deposition and fatty acid composition. Thus, this study was conducted to investigate the expression profile of FASN in mRNA and protein levels using real-time quantitative PCR (RT-qPCR) and western-blot methods. In addition, single nucleotide polymorphisms (SNPs) within FASN in 921 Hu rams with IMF content records were investigated using DNA-pooling sequencing and improved multiple ligase detection reaction (iMLDR) methods. Consequently, the highest mRNA expression level of FASN was observed in the perinephric fat, and the lowest in the liver among the 11 tissues analyzed, while no significant difference was found in mRNA and protein expression levels in longissimus dorsi among individuals with different IMF contents. A total of 10 putative SNPs were identified within FASN, and 9 of them can be genotyped by iMLDR method. Notably, two SNPs were significantly associated with IMF content, including NC_040262.1: g.5157 A > G in intron 5 (p = 0.046) and NC_040262.1: g.9413 T > C in intron 16 (p = 0.041), which supply molecular markers for improving meat quality in sheep breeding.

Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs

PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP^+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP^-/- genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP^-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.

Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle

Objective

In recent years, lncRNAs have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation.

Methods

We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the FPKM values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting FDR was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in KEGG pathways. We randomly selected eight lncRNA genes and validated them by RT-qPCR.

Results

We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the MAPK, Ras and PI3k/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway.

Conclusion

Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F2-Crossbred Bulls

Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. However, in bovines, limited data on miRNA profiling and association with divergent intramuscular fat content, regulated exclusively by genetic parameters, have been reported. Here, a microarray experiment was performed to identify and characterize the miRNA expression pattern in the Musculus longissimus dorsi of F₂-cross (Charolais × German Holstein) bulls with high and low IMF. A total of 38 differentially expressed miRNAs (DE miRNAs), including 33 upregulated and 5 downregulated (corrected p-value ≤ 0.05, FC ≥ ±1.2), were reported. Among DE miRNAs, the upregulated miRNAs miR-105a/b, miR-695, miR-1193, miR-1284, miR-1287-5p, miR-3128, miR-3178, miR-3910, miR-4443, miR-4445 and miR-4745, and the downregulated miRNAs miR-877-5p, miR-4487 and miR-4706 were identified as novel fat deposition regulators. DE miRNAs were further analyzed, along with previously identified differentially expressed genes (DEGs) from the same samples and predicted target genes, using multiple bioinformatic approaches, including target prediction tools and co-expression networks, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We identified DE miRNAs and their gene targets associated with bovine intramuscular adipogenesis, and we provide a basis for further functional investigations.

Genetic Variability in the Loci of FABP4, PPARγ and SCD Genes of Sheep Breeds Raised for Different Purposes

The present study was undertaken to analyse the genetic variation in coding sequences, splicing sites and regulatory sequences of FABP4, PPARγ and SCD genes in five breeds of sheep raised in Poland with different purposes: meat (Suffolk, Ile de France), dairy/prolific (Olkuska sheep, Kołuda) and primitive breeds (Polish Mountain Sheep). To identify genetic variability HRM-PCR, sequencing and PCR-RFLP method were used. Determining the genetic structure of the mentioned genes revealed six SNPs: FABP4 – c.73 + 13A>T and c.348 + 85G>A, PPARγ – c.391 – 66C>T (c.481 – 66C>T) and c.529 + 27G>C (c.619 + 27G>C), SCD – c.*945G>A and c.*1116A>G. For the c.*1116A>G SNP, a potential association with specific sheep body type and breeding purpose was found. In turn, the substitution c.*945G>A located in the regulatory region of the 3'-UTR of the Ovis aries SCD gene was identified for the first time. Based on the relationship demonstrated between sheep body constitution and productive type (dairy, meat) and the polymorphism of the SCD gene, further research is needed. The correlation between c.*1116A>G polymorphism and growth rate, slaughter and carcass value as well as meat quality of lambs needs to be studied in more detail. Such studies may lead to more effective selection processes in sheep breeding in the future.

Differential expression of mRNA-miRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle

In this study, we examined the role of mRNAs and miRNAs in variations in intramuscular fat content in the longissimus dorsi muscle in Xinjiang brown cattle. Two groups of Xinjiang brown cattle with extremely different intramuscular fat content in the longissimus dorsi were selected for combined of miRNA and mRNA analysis using an RNA-Seq. In total, 296 mRNAs and 362 miRNAs were significantly differentially expressed, including 155 newly predicted miRNAs, 275 significantly upregulated genes, 252 significantly upregulated miRNAs, 21 significantly downregulated genes and 110 significantly downregulated miRNAs. The combined miRNA and mRNA analysis identified 96 differentially expressed miRNAs and 27 differentially expressed mRNAs. In all, 47 upregulated miRNAs had a regulatory effect on 14 differentially downregulated target genes, and 49 downregulated miRNAs had a regulatory effect on 13 upregulated target genes. To verify the sequencing results, 10 differentially expressed genes (DEGs) and 10 differentially expressed miRNAs were selected for qRT-PCR. The qRT-PCR results confirmed the sequencing results. The results of this study shed light on the molecular regulation of bovine adipose tissue, which might help with the development of new strategies for improving meat quality and animal productivity in beef cattle to provide healthier meat products for consumers.

Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method

Correct species identification is necessary for meat product quality assurance. Genetic markers are useful tools to accurately determine the animal source of meat products. To better protect yak meat and its products, ten single nucleotide polymorphism (SNP) loci from bovine meat-related genes and one positive control primer set were selected to discriminate meat sourced from yak or cattle. A multiplex allele-specific polymerase chain reaction and capillary electrophoresis method was employed for SNP genotyping. The samples were identified as from yak or cattle based on the number of amplicons. Yak samples generally produced one to three amplicon peaks, and the cattle samples yielded five or more peaks in the electropherogram. This method could be useful to distinguish yak meat from cattle beef, and would protect consumers and yak meat producers.

Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

Objective

The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production.

Methods

Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups.

Results

23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups.

Conclusion

In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

Two Novel SNPs of PPARγ Significantly Affect Weaning Growth Traits of Nanyang Cattle

Peroxisome-proliferator-activated receptor gamma (PPARγ) is a key transcription factor that controls adipocyte differentiation and energy in mammals. Therefore, PPARγ is a potential factor influencing animal growth traits. This study primarily evaluates PPARγ as candidate gene for growth traits of cattle and identifies potential molecular marker for cattle breeding. Per previous studies, PPARγ mRNA was mainly expressed at extremely high levels in adipose tissues as shown by quantitative real-time polymerase chain reaction analysis. Three novel SNPs of the bovine PPARγ gene were identified in 514 individuals from six Chinese cattle breeds: SNP1 (AC_000179.1 g.57386668 C > G) in intron 2 and SNP2 (AC_000179.1 g.57431964 C > T) and SNP3 (AC_000179.1 g.57431994 T > C) in exon 7. The present study also investigated genetic characteristics of these SNP loci in six populations. Association analysis showed that SNP1 and SNP3 loci significantly affect weaning growth traits, especially body weight of Nanyang cattle. These results revealed that SNP1 and SNP3 are potential molecular markers for cattle breeding.