scholarly journals Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0122396 ◽  
Author(s):  
Kai Xing ◽  
Feng Zhu ◽  
Liwei Zhai ◽  
Huijie Liu ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Fat Deposition ◽  
Key Genes ◽  
Genomic Resequencing

scholarly journals Identification of Key Genes Affecting Porcine Fat Deposition Based on Co-Expression Network Analysis of Weighted Genes

2021 ◽  
Author(s):  
Kai Xing ◽  
Huatao Liu ◽  
Fengxia Zhang ◽  
Yibing Liu ◽  
Yong Shi ◽  
...  
Keyword(s):  
Network Analysis ◽  
Production Efficiency ◽  
Fat Deposition ◽  
Rna Seq ◽  
Genetic Studies ◽  
Gene Expression Matrix ◽  
Differential Gene ◽  
Key Genes ◽  
Strong Candidate ◽  
Molecular Regulatory Mechanisms

Abstract Background: Fat deposition is an important economic consideration for pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers' choice of pork. Weighted gene co-expression network analysis (WGCNA) has been shown to be effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low), and to identify the central genes in each of these modules. Results: We used RNA-seq of different pig tissues to construct a gene expression matrix consisting of 12 862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA; the number of genes in these modules ranged from 39 to 3363. We found four co-expression modules were significantly correlated with backfat thickness. A total of 14 genes ( RAD9A , IGF2R , SCAP , TCAP , DGAT1 , GPS2 , IGF1 , MAPK8 , FABP , FABP5 , LEPR , UCP3 , APOF , and FASN ) were found to be related to fat deposition. Conclusions: RAD9A , TCAP , GPS2 , and APOF were found to be the key genes in the four modules according to the degree of gene connectivity. Combining the results of differential gene analysis, APOF was proposed as a strong candidate gene for body size traits. This study explores the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms behind porcine fat deposition.

scholarly journals Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Baojun Li ◽  
Liying Qiao ◽  
Lixia An ◽  
Weiwei Wang ◽  
Jianhua Liu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Fat Deposition ◽  
Adipose Tissues ◽  
Sheep Breeds ◽  
Key Genes

scholarly journals Transcriptional Insights into Key Genes and Pathways Underlying Muscovy Duck Subcutaneous Fat Deposition at Different Developmental Stages

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2099
Author(s):  
Liping Guo ◽  
Congcong Wei ◽  
Li Yi ◽  
Wanli Yang ◽  
Zhaoyu Geng ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Subcutaneous Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Muscovy Duck ◽  
Key Genes

Subcutaneous fat is a crucial trait for waterfowl, largely associated with meat quality and feed conversion rate. In this study, RNA-seq was used to identify differentially expressed genes of subcutaneous adipose tissue among three developmental stages (12, 35, and 66 weeks) in Muscovy duck. A total of 138 and 129 differentially expressed genes (DEGs) were identified between 35 and 12 weeks (wk), and 66 and 35 wk, respectively. Compared with 12 wk, subcutaneous fat tissue at 35 wk upregulated several genes related to cholesterol biosynthesis and fatty acid biosynthesis, including HSD17B7 and MSMO1, while it downregulated fatty acid beta-oxidation related genes, including ACOX1 and ACSL1. Notably, most of the DEGs (92.2%) were downregulated in 66 wk compared with 35 wk, consistent with the slower metabolism of aging duck. Protein network interaction and function analyses revealed GC, AHSG, FGG, and FGA were the key genes for duck subcutaneous fat from adult to old age. Additionally, the PPAR signaling pathway, commonly enriched between the two comparisons, might be the key pathway contributing to subcutaneous fat metabolism among differential developmental stages in Muscovy duck. These results provide several candidate genes and pathways potentially involved in duck subcutaneous fat deposition, expanding our understanding of the molecular mechanisms underlying subcutaneous fat deposition during development.

scholarly journals Integrative Analyses of mRNA Expression Profile Reveal SOCS2 and CISH Play Important Roles in GHR Mutation-Induced Excessive Abdominal Fat Deposition in the Sex-Linked Dwarf Chicken

2021 ◽  
Vol 11 ◽  
Author(s):  
Genghua Chen ◽  
Jiahui Chen ◽  
Jingwen Wu ◽  
Xueyi Ren ◽  
Limin Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Lipid Droplet ◽  
Fatty Acid Metabolism ◽  
Acid Metabolism ◽  
Abdominal Fat ◽  
Fat Deposition ◽  
Recessive Mutation ◽  
Regulatory Pathways ◽  
Key Genes ◽  
Abdominal Fat Deposition

Sex-linked dwarf (SLD) chicken, which is caused by a recessive mutation of the growth hormone receptor (GHR), has been widely used in the Chinese broiler industry. However, it has been found that the SLD chicken has more abdominal fat deposition than normal chicken. Excessive fat deposition not only reduced the carcass quality of the broilers but also reduced the immunity of broilers to diseases. To find out the key genes and the precise regulatory pathways that were involved in the GHR mutation-induced excessive fat deposition, we used high-fat diet (HFD) and normal diet to feed the SLD chicken and normal chicken and analyzed the differentially expressed genes (DEGs) among the four groups. Results showed that the SLD chicken had more abdominal fat deposition and larger adipocytes size than normal chicken and HFD can promote abdominal fat deposition and induce adipocyte hypertrophy. RNA sequencing results of the livers and abdominal fats from the above chickens revealed that many DEGs between the SLD and normal chickens were enriched in fat metabolic pathways, such as peroxisome proliferator-activated receptor (PPAR) signaling, extracellular matrix (ECM)-receptor pathway, and fatty acid metabolism. Importantly, by constructing and analyzing the GHR-downstream regulatory network, we found that suppressor of cytokine signaling 2 (SOCS2) and cytokine-inducible SH2-containing protein (CISH) may involve in the GHR mutation-induced abdominal fat deposition in chicken. The ectopic expression of SOCS2 and CISH in liver-related cell line leghorn strain M chicken hepatoma (LMH) cell and immortalized chicken preadipocytes (ICP) revealed that these two genes can regulate fatty acid metabolism, adipocyte differentiation, and lipid droplet accumulation. Notably, overexpression of SOCS2 and CISH can rescue the hyperactive lipid metabolism and excessive lipid droplet accumulation of primary liver cell and preadipocytes that were isolated from the SLD chicken. This study found some genes and pathways involved in abdominal fat deposition of the SLD chicken and reveals that SOCS2 and CISH are two key genes involved in the GHR mutation-induced excessive fat deposition of the SLD chicken.

scholarly journals Identification of key genes affecting porcine fat deposition based on co-expression network analysis of weighted genes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kai Xing ◽  
Huatao Liu ◽  
Fengxia Zhang ◽  
Yibing Liu ◽  
Yong Shi ◽  
...  
Keyword(s):  
Network Analysis ◽  
Production Efficiency ◽  
Fat Deposition ◽  
Rna Sequences ◽  
Gene Expression Matrix ◽  
Differential Gene ◽  
Key Genes ◽  
Strong Candidate ◽  
Molecular Regulatory Mechanisms ◽  
Core Genes

Abstract Background Fat deposition is an important economic consideration in pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers’ choice of pork. Weighted gene co-expression network analysis (WGCNA) is effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low) and to identify the core genes in each of these modules. Results We used RNA sequences generated in different pig tissues to construct a gene expression matrix consisting of 12,862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA and the number of genes in these modules ranged from 39 to 3,363. Four co-expression modules were significantly correlated with backfat thickness. A total of 16 genes (RAD9A, IGF2R, SCAP, TCAP, SMYD1, PFKM, DGAT1, GPS2, IGF1, MAPK8, FABP, FABP5, LEPR, UCP3, APOF, and FASN) were associated with fat deposition. Conclusions RAD9A, TCAP, SMYD1, PFKM, GPS2, and APOF were the key genes in the four modules based on the degree of gene connectivity. Combining these results with those from differential gene analysis, SMYD1 and PFKM were proposed as strong candidate genes for body size traits. This study explored the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms underlying porcine fat deposition.

Effect of cortisol on neurophysin I/oxytocin and peptidyl glycine-α-amidating mono-oxygenase mRNA expression in bovine luteal and granulosa cells

2013 ◽  
Vol 16 (2) ◽  
pp. 231-239
Author(s):  
A. Ziolkowska ◽  
J. Mlynarczuk ◽  
J. Kotwica
Keyword(s):  
Mrna Expression ◽  
Granulosa Cells ◽  
Molecular Mechanisms ◽  
Hormone Secretion ◽  
Oestrous Cycle ◽  
Luteal Cells ◽  
Ru 486 ◽  
Ovarian Cells ◽  
Key Genes ◽  
Ovary Function

Abstract Cortisol stimulates the synthesis and secretion of oxytocin (OT) from bovine granulosa and luteal cells, but the molecular mechanisms of cortisol action remain unknown. In this study, granulosa cells or luteal cells from days 1-5 and 11-15 of the oestrous cycle were incubated for 4 or 8 h with cortisol (1x10-5, 1x10-7 M). After testing cell viability and hormone secretion (OT, progesterone, estradiol), we studied the effect of cortisol on mRNA expression for precursor of OT (NP-I/OT) and peptidyl glycine-α-amidating mono-oxygenase (PGA). The influence of RU 486 (1x10-5 M), a progesterone receptor blocker and inhibitor of the glucocorticosteroid receptor (GR), on the expression for both genes was tested. Cortisol increased the mRNA expression for NP-I/OT and PGA in granulosa cells and stimulated the expression for NP-I/OT mRNA in luteal cells obtained from days 1-5 and days 11-15 of the oestrous cycle. Expression for PGA mRNA was increased only in luteal cells from days 11-15 of the oestrous cycle. In addition, RU 486 blocked the cortisol-stimulated mRNA expression for NP-I/OT and PGA in both types of cells. These data suggest that cortisol affects OT synthesis and secretion in bovine ovarian cells, by acting on the expression of key genes, that may impair ovary function.

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