Co-inherited novel SNPs of the LIPE gene associated with increased carcass dressing and decreased fat-tail weight in Awassi breed

Screening for genes, miRNAs and transcription factors of adipogenic differentiation and dedifferentiation of mesenchymal stem cells

BACKGROUND

The purpose of present study was to reveal the molecular mechanisms responsible for both adipogenic differentiation and dedifferentiation of mesenchymal stem cells (MSCs).

METHODS

Microarray data GSE36923 were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between adipogenically differentiated cells vs undifferentiated bone marrow-derived MSCs, adipogenically differentiated cells vs dedifferentiated cells samples at day 7 and adipogenically differentiated cells vs dedifferentiated cells samples at day 35 were screened, and overlapped DEGs across the three groups were analyzed. The underlying functions of the upregulated and downregulated DEGs were investigated by Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The protein-protein interaction network was constructed, and hub genes were obtained subsequently. Hub genes were verified with GSE113253 dataset, and then miRNA-gene network and TF-gene network were constructed.

RESULTS

A total of 284 upregulated DEGs and 376 downregulated DEGs overlapped across the three groups. PPAR signaling pathway, AMPK signaling pathway, insulin signaling pathway, carbon metabolism, pyruvate metabolism, fatty acid metabolism, regulation of lipolysis in adipocytes, biosynthesis of amino acids, citrate cycle (TCA cycle) and 2-Oxocarboxylic acid metabolism were the top 10 pathways involving in the upregulated DEGs, and graft-versus-host disease, allograft rejection, viral myocarditis, cell adhesion molecules, phagosome, type I diabetes mellitus, antigen processing and presentation, autoimmune thyroid disease, intestinal immune network for IgA production and rheumatoid arthritis were the top 10 pathways in downregulated DEGs. After validation, the 8 hub genes were IL6, PPARG, CCL2, FASN, CEBPA, ADIPOQ, FABP4 and LIPE. Ten key miRNAs were hsa-mir-27a-3p, hsa-mir-182-5p, hsa-mir-7-5p, hsa-mir-16-5p, hsa-mir-1-3p, hsa-mir-155-5p, hsa-mir-21-3p, hsa-mir-34a-5p, hsa-mir-27a-5p and hsa-mir-30c-5p, and 10 key TFs were TFDP1, GTF2A2, ZNF584, NRF1, ZNF512, NFRKB, CEBPG, KLF16, GLIS2 and MXD4.

CONCLUSION

Our study constructed miRNA-gene network and TF-gene network involved in both adipogenic differentiation and dedifferentiation of MSCs, contributing to enhancing the efficiency of MSCs transplantation in soft tissue defect repair and developing more potent remedies for adipogenesis-related skeletal disorders.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

BACKGROUND

After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.

REVIEW

Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.

CONCLUSIONS

Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.

Comparative Transcriptome Analysis Reveals the Mechanism Associated With Dynamic Changes in Meat Quality of the Longissimus Thoracis Muscle in Tibetan Sheep at Different Growth Stages

Tibetan sheep are mainly distributed in the Qinghai–Tibet Plateau. Its meat is not only essential for the local people but also preferred by the non-inhabitant of this plateau also. To investigate the salient development features and molecular mechanism of the meat difference of LT muscle caused by different growth stages in Tibetan sheep, the carcass performance, meat quality, and comparative transcriptome analysis were performed for investigating the potential molecular mechanism of the meat quality difference of the LT muscle caused by four growth stages [4-months old (4 months), 1.5-years old (1.5 years), 3.5-years old (3.5 years), and 6-years old (6 years)] in the Tibetan sheep. The shear force increased with the increase of age (p < 0.05) while the intramuscular fat (IMF) was the highest at 1.5 y. The AMPK signaling pathway was significantly enriched in the four comparative groups. The weighted gene co-expression network analysis (WGCNA) results showed that the hub genes P4HA2, FBXL4, and PPARA were identified to regulate the meat quality. In summary, 1.5 years was found to be the most suitable slaughter age of the Tibetan sheep which ensured better meat tenderness and higher IMF content. Moreover, the genes LIPE, LEP, ADIPOQ, SCD, and FASN may regulate the transformation of the muscle fiber types through the AMPK signaling pathway, further affecting the meat quality.

Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages

Long noncoding RNA (lncRNA) plays an important regulatory role in mammalian adipogenesis and lipid metabolism. However, their function in the longissimus thoracis (LT) muscle of fatty acid metabolism of Tibetan sheep remains undefined. In this study, fatty acid and fat content in LT muscle of Tibetan sheep were determined, and RNA sequencing was performed to reveal the temporal regularity of lncRNA expression and the effect of lncRNA-miRNA-mRNA ceRNA regulatory network on lipid metabolism of LT muscle in Tibetan sheep at four growth stages (4-month-old, 4 m; 1.5-year-old, 1.5 y; 3.5-year-old, 3.5 y; 6-year-old, 6 y). The results indicated that the intramuscular fat (IMF) content was highest at 1.5 y. Moreover, the monounsaturated fatty acid (MUFA) content in 1.5 y of Tibetan sheep is significantly higher than those of the other groups (P < 0.05), and it was also rich in a variety of polyunsaturated fatty acids (PUFA). A total of 360 differentially expressed lncRNAs (DE lncRNAs) were identified from contiguous period transcriptome comparative groups of 4 m vs. 1.5 y, 1.5 y vs. 3.5 y, 3.5 y vs. 6 y, and 4 m vs. 6 y, respectively. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis found that the target genes in lncRNA trans-mRNA were significantly related to the protein digestion, absorption, and fatty acid biosynthesis pathways (P < 0.05), which demonstrated that DE lncRNA trans-regulated the target genes, and further regulated the growth and development of the LT muscle and intramuscular fatty acid metabolism in Tibetan sheep. We further analyzed the role of the lncRNA-miRNA-mRNA regulatory network in the lipid metabolism of Tibetan sheep. Additionally, GPD2, LIPE (lipase E hormone-sensitive enzyme), TFDP2, CPT1A, ACACB, ADIPOQ, and other mRNA related to fatty acid and lipid metabolism and the corresponding lncRNA-miRNA regulatory pairs were identified. The enrichment analysis of mRNA in the regulatory network found that the AMPK signaling pathway was the most significantly enriched (P = 0.0000112361). Comprehensive transcriptome analysis found that the LIPE, ADIPOQ, ACACB, and CPT1A that were regulated by lncRNA might change the formation of energy metabolism in Tibetan sheep muscle through the AMPK signaling pathway, and oxidized muscle fibers are transformed into glycolytic muscle fibers, reduced IMF content, and the fatty acid profile also changed.

Potential of eight mutations for marker-assisted breeding in Chinese Lulai black pigs

Molecular marker-assisted selection (MAS) provides an efficient tool for pig breeding. In this study, according to the literature, we selected eight effective or causal mutations from eight functional genes, including five causal mutations in PHKG1 (rs330928088), MUC13 (rs319699771), IGF2 (g.3072G>A), VRTN (g.20311_20312ins291) and MYH3 (XM_013981330.2：g.-1805_-1810del) genes, and three effective mutations in LIPE (rs328830166), LEPR (rs45435518) and MC4R (rs81219178) genes, to investigate the potential breeding effect of them in 418 Lulai pigs. The linear model was used to analyze the association between mutations and intramuscular fat (IMF) content, average backfat thickness (ABT) and muscle moisture percent (MMP). The results revealed that among the four effective mutations, only the mutation in the LEPR gene, which affect IMF deposition, was significantly associated with IMF content. However, the other molecular markers were not significantly associated with the affected traits reported in previous studies, and these mutations are ineffective for MAS in the Lulai black pig population. Therefore, causal mutations in PHKG1, IGF2 and VRTN genes, and an effective mutation in LEPR gene could be used as effective breeding makers for MAS in Lulai pigs. These results can provide helpful information for further breeding in Lulai black pigs.