scholarly journals Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 313 ◽  
Author(s):  
Xin Liu ◽  
Jianfei Gong ◽  
Ligang Wang ◽  
Xinhua Hou ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Subcutaneous Fat ◽  
Fat Deposition ◽  
Backfat Thickness ◽  
Feed Conversion ◽  
Protein Coding ◽  
Genes Encoding

Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (AQP9, DKK3, GLYCTK, GLIPR1, and DUSP2) related to fat deposition were found to be strong candidate genes, and mir-31-5p/AQP9 and mir-31-5p/GLIPR1 may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies.

scholarly journals Identification of Candidate Genes that Specifically Regulate Subcutaneous and Intramuscular Fat Deposition Using Transcriptomic and Proteomic Profiles in Dingyuan Pigs

2021 ◽  
Author(s):  
Pan Zhang ◽  
Qinggang Li ◽  
Yijing Wu ◽  
Yawen Zhang ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Candidate Genes ◽  
Metabolic Pathways ◽  
Subcutaneous Fat ◽  
Intramuscular Fat ◽  
Fat Deposition ◽  
Backfat Thickness ◽  
Pathway Enrichment Analysis ◽  
Wide Range

Abstract Background: Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. The Dingyuan pig is a local pig breed in Anhui Province, China, that has great potential for fat deposition. Individuals with extreme subcutaneous fat and intramuscular fat content can be found in this breed, which provides a good study system for investigating the molecular mechanisms regulating these two types of fat deposit.Results: In this study, we used RNA-Seq and tandem mass tags-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high backfat thickness (HBF) and low backfat thickness (LBF) groups. In the high intramuscular fat and low intramuscular fat groups, we found 85 DEGs and 12 DAPs. The gene ontology and KEGG pathway enrichment analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in various metabolic pathways, such as those related to carbohydrates, amino acids, esters, and fatty acids, whereas the DEGs and DAPs of the IMF groups were involved in a wide range of signaling pathways, including metabolic pathways, the insulin pathway, ketone body synthesis and degradation, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters, and fatty acids, we found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes that specifically regulate IMF deposition in Dingyuan pigs.Conclusion: Our data show that subcutaneous fat deposition and IMF deposition are regulated by the same genes, but there are also genes that specifically regulate these two fat depositions. Our data provide insights into the mechanisms of pig fat deposition.

scholarly journals Identification of Candidate Genes that Specifically Regulate Subcutaneous and Intramuscular Fat Deposition Using Transcriptomic and Proteomic Profiles in Dingyuan Pigs

2021 ◽  
Author(s):  
Pan Zhang ◽  
Qinggang Li ◽  
Yijing Wu ◽  
Yawen Zhang ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Candidate Genes ◽  
Metabolic Pathways ◽  
Subcutaneous Fat ◽  
Intramuscular Fat ◽  
Fat Deposition ◽  
Backfat Thickness ◽  
Pathway Enrichment Analysis ◽  
Wide Range

Abstract Background: Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. The Dingyuan pig is a local pig breed in Anhui Province, China, that has great potential for fat deposition. Individuals with extreme subcutaneous fat and intramuscular fat content can be found in this breed, which provides a good study system for investigating the molecular mechanisms regulating these two types of fat deposit.Results: In this study, we used RNA-Seq and tandem mass tags-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high backfat thickness (HBF) and low backfat thickness (LBF) groups. In the high intramuscular fat and low intramuscular fat groups, we found 85 DEGs and 12 DAPs. The gene ontology and KEGG pathway enrichment analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in various metabolic pathways, such as those related to carbohydrates, amino acids, esters, and fatty acids, whereas the DEGs and DAPs of the IMF groups were involved in a wide range of signaling pathways, including metabolic pathways, the insulin pathway, ketone body synthesis and degradation, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters, and fatty acids, we found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes that specifically regulate IMF deposition in Dingyuan pigs.Conclusion: Our data show that subcutaneous fat deposition and IMF deposition are regulated by the same genes, but there are also genes that specifically regulate these two fat depositions. Our data provide insights into the mechanisms of pig fat deposition.

scholarly journals Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

2019 ◽  
Author(s):  
Yan-Nong Cui ◽  
Fang-Zhen Wang ◽  
Cheng-Hang Yang ◽  
Jian-Zhen Yuan ◽  
Huan Guo ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Assimilation Efficiency ◽  
Carbon Assimilation ◽  
Inorganic Ions ◽  
Ros Scavenging ◽  
Genes Encoding

Abstract Background: Pugionium cornutum is a xerophytic plant that primarily adapts to salt stress by accumulating inorganic ions (e.g., Cl-) for osmoregulation, improving its reactive oxygen species (ROS)-scavenging ability and maintaining high photosynthetic carbon assimilation efficiency, but the associated molecular mechanisms still remain unclear. Results: Here, we present an analysis of gene responses to salt stress based on the transcriptome of P. cornutum exposed to 50 mM NaCl treatment. The data revealed that, after NaCl treatment for 6 or 24 h, the transcript levels of multiple genes encoding proteins facilitating Cl- accumulation and NO3- homeostasis such as SLAH1, CLCg, CCC1, and NPF6.4, as well as the transport of other major inorganic osmoticums were significantly upregulated in roots and shoots, which should be favorable to enhancing osmotic adjustment capacity and maintaining the plant uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which should be beneficial for mitigating salt-induced oxidative damage to the cell metabolism. Meanwhile, many genes encoding components of the photosynthetic electron transport and carbon fixation enzymes were significantly upregulated in shoots after salt treatment, possibly resulting in a high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes probably regulating the abovementioned processes were found. Conclusion: Candidate genes involved in salt tolerance of P. cornutum were identified, which lays a preliminary foundation for clarifying the molecular mechanism of the xerophytes adapting to harsh environments.

scholarly journals Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Kejun Wang ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

The effect of plane of nutrition on the performance and carcass characteristics of pigs slaughtered at 100 kg live weight

1972 ◽  
Vol 78 (3) ◽  
pp. 449-455 ◽  
Author(s):  
N. Walker ◽  
I. H. Heaney ◽  
D. H. McNally
Keyword(s):  
Feed Intake ◽  
Subcutaneous Fat ◽  
Carcass Characteristics ◽  
Live Weight ◽  
Backfat Thickness ◽  
Muscle Quality ◽  
Feed Conversion ◽  
Weight Range ◽  
Commercial Practice ◽  
Daily Gain

SUMMARYFour equally spaced feeding levels, estimated to cover the range of commercial practice, were examined using a total of 208 pigs over the live-weight range 28–100 kg. The pigs were penned in groups of six or eight and were balanced for sex within pens. Three centres participated in the experiment contributing five, two and one replicates respectively.Efficiency of feed conversion was not significantly affected over the range of feed intakes studied, thus daily gain was linearly related to feed intake. A 10 decrease in feed intake increased killing-out percentage by 0·3 unit and decreased backfat thickness by 1 mm at both the shoulder and mid rump. The corresponding changes in the percentages of subcutaneous fat plus skin and meat were similar in magnitude at approximately 0·85 unit.Muscle quality was reduced with higher feed intakes but weight of liver, as increased. Details of other offal weights and carcass measurements are given.

scholarly journals Established and Emerging Mechanisms in the Pathogenesis of Arrhythmogenic Cardiomyopathy: A Multifaceted Disease

2020 ◽  
Vol 21 (17) ◽  
pp. 6320
Author(s):  
Shanshan Gao ◽  
Deepa Puthenvedu ◽  
Raffaella Lombardi ◽  
Suet Nee Chen
Keyword(s):  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Autoimmune Response ◽  
Arrhythmogenic Cardiomyopathy ◽  
Cellular Mechanisms ◽  
Paracrine Factors ◽  
Epicardial Cells ◽  
Genes Encoding ◽  
Advanced Stages ◽  
Canonical Wnt

Arrhythmogenic cardiomyopathy (ACM) is a heritable myocardial disease that manifests with cardiac arrhythmias, syncope, sudden cardiac death, and heart failure in the advanced stages. The pathological hallmark of ACM is a gradual replacement of the myocardium by fibroadiposis, which typically starts from the epicardium. Molecular genetic studies have identified causal mutations predominantly in genes encoding for desmosomal proteins; however, non-desmosomal causal mutations have also been described, including genes coding for nuclear proteins, cytoskeleton componentsand proteins involved in excitation-contraction coupling. Despite the poor prognosis, currently available treatments can only partially control symptoms and to date there is no effective therapy for ACM. Inhibition of the canonical Wnt/β-catenin pathway and activation of the Hippo and the TGF-β pathways have been implicated in the pathogenesis of ACM. Yet, our understanding of the molecular mechanisms involved in the development of the disease and the cell source of fibroadiposis remains incomplete. Elucidation of the pathogenesis of the disease could facilitate targeted approaches for treatment. In this manuscript we will provide a comprehensive review of the proposed molecular and cellular mechanisms of the pathogenesis of ACM, including the emerging evidence on abnormal calcium homeostasis and inflammatory/autoimmune response. Moreover, we will propose novel hypothesis about the role of epicardial cells and paracrine factors in the development of the phenotype. Finally, we will discuss potential innovative therapeutic approaches based on the growing knowledge in the field.

Mendelian hypertension with brachydactyly as a molecular genetic lesson in regulatory physiology

2003 ◽  
Vol 285 (4) ◽  
pp. R709-R714 ◽  
Author(s):  
Friedrich C. Luft ◽  
Okan Toka ◽  
Hakan R. Toka ◽  
Jens Jordan ◽  
Sylvia Bähring
Keyword(s):  
Essential Hypertension ◽  
Molecular Mechanisms ◽  
Antihypertensive Drugs ◽  
Molecular Genetic ◽  
Plasma Renin ◽  
Salt Sensitivity ◽  
Ventrolateral Medulla ◽  
Sulfonylurea Receptor ◽  
Genetic Syndrome ◽  
Genes Encoding

Mendelian forms of hypertension have delivered a treasure trove of novel genes. To date, the molecular mechanisms of five such syndromes have been largely clarified, including glucocorticoid-remediable aldosteronism, Liddle's syndrome, apparent mineralocorticoid excess, an activating mutation of the mineralocorticoid receptor, and pseudohypoaldosteronism type 2. Each of these conditions features salt sensitivity with increased sodium and volume reabsorption by the kidney and low plasma renin activity. None of the gene loci for these syndromes has been convincingly linked to hypertension in the general population. We are investigating kindreds who have autosomal-dominant hypertension and brachydactyly. Affected persons invariably have both anomalies. The hypertension is severe and results in death at about age 50 years from stroke. The condition resembles essential hypertension, because renin, aldosterone, and norepinephrine responses are normal and no salt sensitivity is present. The response to antihypertensive drugs is general. Another feature is diminished baroreflex sensitivity with markedly impaired blood pressure buffering. Furthermore, the ventrolateral medulla may be compromised in these patients, because neurovascular anomalies are a regular finding. We mapped the gene(s) for this disease to chromosome 12p and narrowed the chromosomal region by studying more affected families. Interestingly, the same locus was recently mapped in Chinese families with essential hypertension. Our 3-centimorgan region contains genes encoding a phosphodiesterase, an ATP-dependent potassium channel, and its regulator the sulfonylurea receptor 2. Screening of the coding regions revealed that none of these candidate genes harbor obvious mutations; however, other genetic mechanisms may nevertheless compromise their function. Our study underscores the importance of regulatory physiology to the understanding of a complex genetic syndrome.

Transcriptome analysis of the ischemia-reperfused remodeling myocardium: temporal changes in inflammation and extracellular matrix

2006 ◽  
Vol 25 (3) ◽  
pp. 364-374 ◽  
Author(s):  
Sashwati Roy ◽  
Savita Khanna ◽  
Donald E. Kuhn ◽  
Cameron Rink ◽  
Willis T. Williams ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Acute Myocardial Infarction ◽  
Extracellular Matrix ◽  
Candidate Genes ◽  
Dna Microarrays ◽  
Molecular Mechanisms ◽  
Acute Infarction ◽  
Genes Encoding ◽  
Apoptosis And Inflammation ◽  
Microarray Studies

cDNA microarray analysis was performed to screen 15,000 genes and expressed sequence tags (ESTs) to identify changes in the ischemia-reperfused (I-R) rat myocardial transcriptome in the early ( day 2) and late ( day 7) inflammatory phases of acute myocardial infarction. Lists of candidate genes that were affected by I-R transiently (2 or 7 days only) or on a more sustained basis (2 and 7 days) were derived. The candidate genes represented three major functional categories: extracellular matrix, apoptosis, and inflammation. To expand on the findings from microarray studies that dealt with the two above-mentioned time points, tissues collected from days 0, 0.25, 2, 3, 5, and 7 after reperfusion were examined. Acute myocardial infarction resulted in upregulation of IL-6 and IL-18. Genes encoding extracellular matrix proteins such as types I and III collagen were upregulated in day 2, and that response progressively grew stronger until day 7 after I-R. Comparable response kinetics was exhibited by the candidate genes of the apoptosis category. Caspases-2, -3, and -8 were induced in response to acute infarction. Compared with the myocardial tissue from the sham-operated rats, tissue collected from the infarct region stained heavily positive for the presence of active caspase-3. Laser microdissection and pressure catapulting technology was applied to harvest infarct and adjacent noninfarct control tissue from a microscopically defined region in the rat myocardium. Taken together, this work presents the first evidence gained from the use of DNA microarrays to understand the molecular mechanisms implicated in the early and late inflammatory phases of the I-R heart.

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 Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea

PLoS Genetics ◽  
2021 ◽  
Vol 17 (5) ◽  
pp. e1009530
Author(s):  
Yinnan Mu ◽  
Chao Bian ◽  
Ruoyu Liu ◽  
Yuguang Wang ◽  
Guangming Shao ◽  
...  
Keyword(s):  
Hydrostatic Pressure ◽  
Food Supply ◽  
Deep Sea ◽  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Extreme Environment ◽  
Protein Coding ◽  
Evolutionary Features ◽  
Genes Encoding ◽  
Show Evidence

Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. The evolutionary adaptations that allow vertebrates to survive in this extreme environment are poorly understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS), which was captured at a depth of ~7,000 m in the Yap Trench. The final YHS genome assembly was 731.75 Mb, with a contig N50 of 0.75 Mb and a scaffold N50 of 1.26 Mb. We predicted 24,329 protein-coding genes in the YHS genome, and 24,265 of these genes were successfully functionally annotated. Phylogenetic analyses suggested that YHS diverged from a Mariana Trench snailfish approximately 0.92 million years ago. Many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, possibly helping to maintain the integrity of DNA under increased hydrostatic pressure. The levels of trimethylamine N-oxide (TMAO), a potent protein stabilizer, are much higher in the muscles of YHS than in those of shallow-water fish. This difference is perhaps due to the five copies of the TMAO-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) in the YHS genome and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut. Thus, the high TMAO content might help YHS adapt to high hydrostatic pressure by improving protein stability. Additionally, the evolutionary features of the YHS genes encoding sensory-related proteins are consistent with the scarce food supply and darkness in the hadal environments. These results clarify the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and provide valuable genomic resources for in-depth investigations of hadal biology.

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