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1.
BMC Genomics ; 20(1): 1033, 2019 Dec 30.
Article in English | MEDLINE | ID: mdl-31888468

ABSTRACT

BACKGROUND: Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a multi-tissue transcriptomic analysis. Study was designed to compare effects of the nutritional intervention in two layer chicken lines divergently selected for residual feed intake. RESULTS: Chicken adapted to the diet in terms of production by significantly increasing their feed intake and decreasing their body weight and body fat composition, while their egg production was unchanged. No significant interaction was observed between diet and line for the production traits. The low energy diet had no effect on adipose tissue and liver transcriptomes. By contrast, the nutritional challenge affected the blood transcriptome and, more severely, the hypothalamus transcriptome which displayed 2700 differentially expressed genes. In this tissue, the low-energy diet lead to an over-expression of genes related to endocannabinoid signaling (CN1R, NAPE-PLD) and to the complement system, a part of the immune system, both known to regulate feed intake. Both mechanisms are associated to genes related polyunsaturated fatty acids synthesis (FADS1, ELOVL5 and FADS2), like the arachidonic acid, a precursor of anandamide, a key endocannabinoid, and of prostaglandins, that mediate the regulatory effects of the complement system. A possible regulatory role of NR1H3 (alias LXRα) has been associated to these transcriptional changes. The low-energy diet further affected brain plasticity-related genes involved in the cholesterol synthesis and in the synaptic activity, revealing a link between nutrition and brain plasticity. It upregulated genes related to protein synthesis, mitochondrial oxidative phosphorylation and fatty acid oxidation in the hypothalamus, suggesting reorganization in nutrient utilization and biological synthesis in this brain area. CONCLUSIONS: We observed a complex transcriptome modulation in the hypothalamus of chicken in response to low-energy diet suggesting numerous changes in synaptic plasticity, endocannabinoid regulation, neurotransmission, lipid metabolism, mitochondrial activity and protein synthesis. This global transcriptomic reprogramming could explain the adaptive behavioral response (i.e. increase of feed intake) of the animals to the low-energy content of the diet.


Subject(s)
Caloric Restriction , Diet , Energy Metabolism , Adaptation, Physiological , Animals , Body Composition , Chickens , Gene Expression Regulation , Hypothalamus , Lipid Metabolism , Models, Biological , Quantitative Trait, Heritable , Transcriptome
2.
BMC Genomics ; 19(1): 187, 2018 03 07.
Article in English | MEDLINE | ID: mdl-29514634

ABSTRACT

BACKGROUND: Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have recently shown that meat-type chicken source is prone to adapt to dietary starch substitution with fat and fiber. The aim of this study was to better understand the molecular mechanisms of this adaptation to changes in dietary energy sources through the fine characterization of transcriptomic changes occurring in three major metabolic tissues - liver, adipose tissue and muscle - as well as in circulating blood cells. RESULTS: We revealed the fine-tuned regulation of many hepatic genes encoding key enzymes driving glycogenesis and de novo fatty acid synthesis pathways and of some genes participating in oxidation. Among the genes expressed upon consumption of a high-fat, high-fiber diet, we highlighted CPT1A, which encodes a key enzyme in the regulation of fatty acid oxidation. Conversely, the repression of lipogenic genes by the high-fat diet was clearly associated with the down-regulation of SREBF1 transcripts but was not associated with the transcript regulation of MLXIPL and NR1H3, which are both transcription factors. This result suggests a pivotal role for SREBF1 in lipogenesis regulation in response to a decrease in dietary starch and an increase in dietary PUFA. Other prospective regulators of de novo hepatic lipogenesis were suggested, such as PPARD, JUN, TADA2A and KAT2B, the last two genes belonging to the lysine acetyl transferase (KAT) complex family regulating histone and non-histone protein acetylation. Hepatic glycogenic genes were also down-regulated in chickens fed a high-fat, high-fiber diet compared to those in chickens fed a starch-based diet. No significant dietary-associated variations in gene expression profiles was observed in the other studied tissues, suggesting that the liver mainly contributed to the adaptation of birds to changes in energy source and nutrients in their diets, at least at the transcriptional level. Moreover, we showed that PUFA deposition observed in the different tissues may not rely on transcriptional changes. CONCLUSION: We showed the major role of the liver, at the gene expression level, in the adaptive response of chicken to dietary starch substitution with fat and fiber.


Subject(s)
Diet, High-Fat/veterinary , Dietary Fiber/administration & dosage , Lipogenesis , Liver/metabolism , Starch/administration & dosage , Animals , Chickens , Gene Expression Regulation , Liver/drug effects , Meat , Transcription, Genetic , Transcriptome
3.
Cell Mol Life Sci ; 75(6): 975-987, 2018 03.
Article in English | MEDLINE | ID: mdl-28988292

ABSTRACT

In the course of the last decades, metabolism research has demonstrated that adipose tissue is not an inactive tissue. Rather, adipocytes are key actors of whole body energy homeostasis. Numerous novel regulators of adipose tissue differentiation and function have been identified. With the constant increase of obesity and associated disorders, the interest in adipose tissue function alterations in the XXIst century has become of paramount importance. Recent data suggest that adipocyte differentiation, adipose tissue browning and mitochondrial function, lipogenesis and lipolysis are strongly modulated by the cell division machinery. This review will focus on the function of cell cycle regulators in adipocyte differentiation, adipose tissue function and whole body energy homeostasis; with particular attention in mouse studies.


Subject(s)
Adipose Tissue/metabolism , Cell Cycle Proteins/metabolism , Energy Metabolism , Animals , Cell Cycle Checkpoints , Cell Cycle Proteins/genetics , Cyclin-Dependent Kinase Inhibitor Proteins/genetics , Cyclin-Dependent Kinase Inhibitor Proteins/metabolism , Cyclin-Dependent Kinases/genetics , Cyclin-Dependent Kinases/metabolism , Cyclins/genetics , Cyclins/metabolism , E2F Transcription Factors/genetics , E2F Transcription Factors/metabolism , Humans
4.
Animal ; 9(10): 1643-52, 2015 Oct.
Article in English | MEDLINE | ID: mdl-25959107

ABSTRACT

The increasing use of unconventional feedstuffs in chicken's diets results in the substitution of starch by lipids as the main dietary energy source. To evaluate the responses of genetically fat or lean chickens to these diets, males of two experimental lines divergently selected for abdominal fat content were fed isocaloric, isonitrogenous diets with either high lipid (80 g/kg), high fiber (64 g/kg) contents (HL), or low lipid (20 g/kg), low fiber (21 g/kg) contents (LL) from 22 to 63 days of age. The diet had no effect on growth performance and did not affect body composition evaluated at 63 days of age. Glycolytic and oxidative energy metabolisms in the liver and glycogen storage in liver and Sartorius muscle at 63 days of age were greater in chicken fed LL diet compared with chicken fed HL diet. In Pectoralis major (PM) muscle, energy metabolisms and glycogen content were not different between diets. There were no dietary-associated differences in lipid contents of the liver, muscles and abdominal fat. However, the percentages of saturated (SFA) and monounsaturated fatty acids (MUFA) in tissue lipids were generally higher, whereas percentages of polyunsaturated fatty acids (PUFA) were lower for diet LL than for diet HL. The fat line had a greater feed intake and average daily gain, but gain to feed ratio was lower in that line compared with the lean line. Fat chickens were heavier than lean chickens at 63 days of age. Their carcass fatness was higher and their muscle yield was lower than those of lean chickens. The oxidative enzyme activities in the liver were lower in the fat line than in the lean line, but line did not affect energy metabolism in muscles. The hepatic glycogen content was not different between lines, whereas glycogen content and glycolytic potential were higher in the PM muscle of fat chickens compared with lean chickens. Lipid contents in the liver, muscles and abdominal fat did not differ between lines, but fat chickens stored less MUFA and more PUFA in abdominal fat and muscles than lean chickens. Except for the fatty acid composition of liver and abdominal fat, no interaction between line and diet was observed. In conclusion, the amount of lipids stored in muscles and fatty tissues by lean or fat chickens did not depend on the dietary energy source.


Subject(s)
Chickens/physiology , Diet/veterinary , Energy Metabolism , Fatty Acids/metabolism , Lipid Metabolism , Abdominal Fat/metabolism , Adipose Tissue/metabolism , Animals , Body Composition , Dietary Fiber/metabolism , Fatty Acids, Monounsaturated/metabolism , Fatty Acids, Unsaturated/metabolism , Glycogen/metabolism , Lipids , Liver/metabolism , Male , Muscle, Skeletal/metabolism
5.
J Anim Sci ; 93(1): 107-16, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25568361

ABSTRACT

Excessive deposition of body fat is detrimental to production efficiency. The aim of this study was to provide plasma indicators of chickens' ability to store fat. From 3 to 9 wk of age, chickens from 2 experimental lines exhibiting a 2.5-fold difference in abdominal fat content and fed experimental diets with contrasted feed energy sources were compared. The diets contained 80 vs. 20 g of lipids and 379 vs. 514 g of starch per kg of feed, respectively, but had the same ME and total protein contents. Cellulose was used to dilute energy in the high-fat diet. At 9 wk of age, the body composition was analyzed and blood samples were collected. A metabolome-wide approach based on proton nuclear magnetic resonance spectroscopy was associated with conventional measurements of plasma parameters. A metabolomics approach showed that betaine, glutamine, and histidine were the most discriminating metabolites between groups. Betaine, uric acid, triglycerides, and phospholipids were positively correlated (r > 0.3; P < 0.05) and glutamine, histidine, triiodothyronine, homocysteine, and ß-hydroxybutyrate were negatively correlated (r < -0.3; P < 0.05) with relative weight of abdominal fat and/or fat situated at the top of external face of the thigh. The combination of plasma free fatty acids, total cholesterol, phospholipid, ß-hydroxybutyrate, glutamine, and methionine levels accounted for 74% of the variability of the relative weight of abdominal fat. On the other hand, the combination of plasma triglyceride and homocysteine levels accounted for 37% of the variability of fat situated at the top of external face of the thigh. The variations in plasma levels of betaine, homocysteine, uric acid, glutamine, and histidine suggest the implication of methyl donors in the control of hepatic lipid synthesis and illustrate the interplay between AA, glucose, and lipid metabolisms in growing chickens.


Subject(s)
Biomarkers/blood , Body Composition/physiology , Chickens/metabolism , Diet, High-Fat/veterinary , Lipid Metabolism/physiology , Lipids/biosynthesis , 3-Hydroxybutyric Acid/metabolism , Abdominal Fat/metabolism , Adipose Tissue/metabolism , Animals , Betaine/blood , Body Weight , Cholesterol/blood , Fatty Acids, Nonesterified/blood , Liver/metabolism , Triglycerides/blood
6.
Anim Genet ; 46(1): 82-6, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25515399

ABSTRACT

The number of polymorphisms identified with next-generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole-genome resequencing (WGS). For this reason, capture resequencing is used for studies focusing on only some specific regions of the genome. However, several biases in capture resequencing are known to have a negative impact on the sensitivity of SNP detection. Within this framework, the aim of this study was to compare the accuracy of WGS and capture resequencing on SNP detection and genotype calling, which differ in terms of both sequencing depth and biases. Indeed, we have evaluated the SNP calling and genotyping accuracy in a WGS dataset (13X) and in a capture resequencing dataset (87X) performed on 11 individuals. The percentage of SNPs not identified due to a sevenfold sequencing depth decrease was estimated at 7.8% using a down-sampling procedure on the capture sequencing dataset. A comparison of the 87X capture sequencing dataset with the WGS dataset revealed that capture-related biases were leading with the loss of 5.2% of SNPs detected with WGS. Nevertheless, when considering the SNPs detected by both approaches, capture sequencing appears to achieve far better SNP genotyping, with about 4.4% of the WGS genotypes that can be considered as erroneous and even 10% focusing on heterozygous genotypes. In conclusion, WGS and capture deep sequencing can be considered equivalent strategies for SNP detection, as the rate of SNPs not identified because of a low sequencing depth in the former is quite similar to SNPs missed because of method biases of the latter. On the other hand, capture deep sequencing clearly appears more adapted for studies requiring great accuracy in genotyping.


Subject(s)
Genotyping Techniques/methods , High-Throughput Nucleotide Sequencing/methods , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods , Animals , Chickens/genetics , Genome , Genotype
7.
J Anim Sci ; 92(11): 4865-77, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25253805

ABSTRACT

The use and partition of feed energy are key elements in productive efficiency of pigs. This study aimed to determine whether dietary energy sources affect the partition of body lipids and tissue biochemical pathways of energy use between pigs differing in feed efficiency. Forty-eight barrows (pure Large White) from two divergent lines selected for residual feed intake (RFI), a measure of feed efficiency, were compared. From 74 d to 132 ± 0.5 d of age, pigs (n = 12 by line and by diet) were offered diets with equal protein and ME contents. A low fat, low fiber diet (LF) based on cereals and a high fat, high fiber diet (HF) where vegetal oils and wheat straw were used to partially substitute cereals, were compared. Irrespective of diet, gain to feed was 10% better (P < 0.001), and carcass yield was greater (+2.3%; P < 0.001) in the low RFI compared with the high RFI line; the most-efficient line was also leaner (+3.2% for loin proportion in the carcass, P < 0.001). In both lines, ADFI and ADG were lower when pigs were fed the HF diet (-12.3% and -15%, respectively, relatively to LF diet; P < 0.001). Feeding the HF diet reduced the perirenal fat weight and backfat proportion in the carcass to the same extent in both lines (-27% on average; P < 0.05). Lipid contents in backfat and LM also declined (-5% and -19%, respectively; P < 0.05) in pigs offered the HF diet. The proportion of saturated fatty acids (FA) was lower, but the percentage of PUFA, especially the EFA C18:2 and C18:3, was greater (P < 0.001) in backfat of HF-fed pigs. In both lines, these changes were associated with a marked decrease (P < 0.001) in the activities of two lipogenic enzymes, the fatty acid synthase (FASN) and the malic enzyme, in backfat. For the high RFI line, the hepatic lipid content was greater (P < 0.05) in pigs fed the HF diet than in pigs fed the LF diet, despite a reduced FASN activity (-32%; P < 0.001). In both lines, the HF diet also led to lower glycogen content (-70%) and lower glucokinase activity (-15%; P < 0.05) in the liver. These results show that dietary energy sources modified the partition of energy between liver, adipose tissue, and muscle in a way that was partly dependent of the genetics for feed efficiency, and changed the activity levels of biochemical pathways involved in lipid and glucose storage in tissues.


Subject(s)
Body Composition/physiology , Diet/veterinary , Energy Intake/physiology , Energy Metabolism/physiology , Lipid Metabolism/physiology , Metabolic Networks and Pathways/physiology , Swine/growth & development , Adipose Tissue/metabolism , Animals , Body Composition/drug effects , Body Weight/physiology , Dietary Fats/pharmacology , Dietary Fiber/pharmacology , Energy Metabolism/drug effects , Fatty Acid Synthases/physiology , Lipid Metabolism/drug effects , Liver/metabolism , Male , Metabolic Networks and Pathways/drug effects , Muscle, Skeletal/metabolism , Swine/genetics , Swine/physiology
8.
J Dairy Sci ; 95(9): 4989-5000, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22916903

ABSTRACT

Microarray analysis was used to identify genes whose expression in the mammary gland of Holstein-Friesian dairy cows was affected by the nonconservative Ala to Lys amino acid substitution at position 232 in exon VIII of the diacylglycerol-O-transferase 1 (DGAT1) gene. Mammary gland biopsies of 9 homozygous Ala cows, 13 heterozygous cows (Ala/Lys), and 4 homozygous Lys cows in midlactation were taken. Microarray ANOVA and factor analysis for multiple testing methods were used as statistical methods to associate the expression level of the genes present on Affymetrix bovine genome arrays (Affymetrix Inc., Santa Clara, CA) with the DGAT1 gene polymorphism. The data was also analyzed at the level of functional modules by gene set enrichment analysis. In this small-scale experimental setting, DGAT1 gene polymorphism did not modify milk yield and composition significantly, although expected changes occurred in the yields of C14:0, cis-9 C16:1, and long-chain fatty acids. Diacylglycerol-O-transferase 1 gene polymorphism affected the expression of 30 annotated genes related to cell growth, proliferation, and development, remodeling of the tissue, cell signaling and immune system response. Furthermore, the main affected functional modules were related to energy metabolism (lipid biosynthesis, oxidative phosphorylation, electron transport chain, citrate cycle, and propanoate metabolism), protein degradation (proteosome-ubiquitin pathways), and the immune system. We hypothesize that the observed differences in transcriptional activity reflect counter mechanisms of mammary gland tissue to respond to changes in milk fatty acid concentration or composition, or both.


Subject(s)
Diacylglycerol O-Acyltransferase/genetics , Genetic Pleiotropy/genetics , Mammary Glands, Animal/metabolism , Amino Acid Substitution/genetics , Amino Acid Substitution/physiology , Animals , Cattle/genetics , Cattle/metabolism , Diacylglycerol O-Acyltransferase/physiology , Female , Gene Expression Regulation, Enzymologic/genetics , Gene Expression Regulation, Enzymologic/physiology , Genetic Pleiotropy/physiology , Genotyping Techniques/veterinary , Heterozygote , Homozygote , Lactation/genetics , Lactation/metabolism , Oligonucleotide Array Sequence Analysis/veterinary , Reverse Transcriptase Polymerase Chain Reaction/veterinary
9.
Nucleic Acids Res ; 39(Web Server issue): W328-33, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21596783

ABSTRACT

AnnotQTL is a web tool designed to aggregate functional annotations from different prominent web sites by minimizing the redundancy of information. Although thousands of QTL regions have been identified in livestock species, most of them are large and contain many genes. This tool was therefore designed to assist the characterization of genes in a QTL interval region as a step towards selecting the best candidate genes. It localizes the gene to a specific region (using NCBI and Ensembl data) and adds the functional annotations available from other databases (Gene Ontology, Mammalian Phenotype, HGNC and Pubmed). Both human genome and mouse genome can be aligned with the studied region to detect synteny and segment conservation, which is useful for running inter-species comparisons of QTL locations. Finally, custom marker lists can be included in the results display to select the genes that are closest to your most significant markers. We use examples to demonstrate that in just a couple of hours, AnnotQTL is able to identify all the genes located in regions identified by a full genome scan, with some highlighted based on both location and function, thus considerably increasing the chances of finding good candidate genes. AnnotQTL is available at http://annotqtl.genouest.org.


Subject(s)
Livestock/genetics , Molecular Sequence Annotation , Quantitative Trait Loci , Software , Animals , Cattle , Genomics/methods , Humans , Internet , Mice
10.
Gene ; 470(1-2): 7-11, 2011 Jan 01.
Article in English | MEDLINE | ID: mdl-20837115

ABSTRACT

In this work we analyzed the transcriptome profiles of chicken hepatoma cells (LMH) in response to T0901317, a pharmacological agonist of the liver X receptor (LXR). Through an in silico search for LXRE (LXR response element) consensus sequences in the promoter of genes whose expression was shown to be sensitive to TO901317, we identified a LXRE in the promoter of the LPCAT3 (lysophosphatidylcholine acyltransferase 3). This motif is highly conserved between species. We further investigated the regulation of this gene and showed that the expression of LPCAT3 was induced both in chicken and human hepatoma cells (LMH and HuH-7, respectively) in response to T0901317. Transactivation and electrophoretic mobility shift assays allowed us to locate a functional LXRE in the chicken LPCAT3 promoter. Altogether these data evidence for the first time that the chicken LPCAT3 gene is a direct target of LXR and therefore suggest a new role for LXR in phospholipid homeostasis.


Subject(s)
1-Acylglycerophosphocholine O-Acyltransferase/genetics , Orphan Nuclear Receptors/metabolism , Animals , Cell Line, Tumor , Chickens , Fatty Acids/metabolism , Gene Expression Profiling , Humans , Hydrocarbons, Fluorinated/pharmacology , Liver X Receptors , Orphan Nuclear Receptors/agonists , Sulfonamides/pharmacology
11.
Poult Sci ; 88(12): 2628-35, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19903962

ABSTRACT

Liver X receptor alpha (LXRalpha), also referred to as nuclear receptor subfamily 1, group H, member 3 is a member of the nuclear hormone receptor superfamily, and has recently been shown to act as a master transcription factor governing hepatic lipogenesis in mammals. Liver X receptor alpha directly regulates both the expression of other lipogenic transcription factors and the expression of lipogenic enzymes, thereby enhancing hepatic fatty acid synthesis (FASN). In birds, like in humans, fatty acid synthesis primarily occurs in the liver. Whether LXRalpha is involved in hepatic regulation of lipogenic genes remained to be investigated in this species. Here we show that fatty acid synthase and the expression of other lipogenic genes (sterol regulatory element binding protein 1 and steroyl coenzyme A desaturase 1) are induced in chicken hepatoma cells in response to a pharmacological liver X receptor agonist, T0901317. A detailed analysis of the chicken FASN promoter revealed a functional liver X response element. These data define the chicken FASN gene as a direct target of LXRalpha and further expand the role of LXRalpha as a regulator of lipid metabolism in this species.


Subject(s)
Fatty Acid Synthases/metabolism , Orphan Nuclear Receptors/metabolism , Amino Acid Sequence , Animals , Cells, Cultured , Chickens , Fatty Acid Synthases/genetics , Hydrocarbons, Fluorinated/pharmacology , Liver X Receptors , Molecular Sequence Data , Orphan Nuclear Receptors/agonists , Sulfonamides/pharmacology
12.
J Theor Biol ; 261(2): 266-78, 2009 Nov 21.
Article in English | MEDLINE | ID: mdl-19635486

ABSTRACT

The purpose of this study is to identify the hierarchy of importance amongst pathways involved in fatty acid (FA) metabolism and their regulators in the control of hepatic FA composition. A modeling approach was applied to experimental data obtained during fasting in PPARalpha knockout (KO) mice and wild-type mice. A step-by-step procedure was used in which a very simple model was completed by additional pathways until the model fitted correctly the measured quantities of FA in the liver. The resulting model included FA uptake by the liver, FA oxidation, elongation and desaturation of FA, which were found active in both genotypes during fasting. From the model analysis we concluded that PPARalpha had a strong effect on FA oxidation. There were no indications that this effect changes during the fasting period, and it was thus considered to be constant. In PPARalpha KO mice, FA uptake was identified as the main pathway responsible for FA variation in the liver. The models showed that FA were oxidized at a constant and small rate, whereas desaturation of FA also occurred during fasting. The latter observation was rather unexpected, but was confirmed experimentally by the measurement of delta-6-desaturase mRNA using real-time quantitative PCR (QPCR). These results confirm that mathematical models can be a useful tool in identifying new biological hypotheses and nutritional routes in metabolism.


Subject(s)
Fasting/metabolism , Fatty Acids/metabolism , Liver/metabolism , Models, Biological , PPAR alpha/physiology , Animals , Gene Expression Regulation/physiology , Genotype , Linoleoyl-CoA Desaturase/biosynthesis , Linoleoyl-CoA Desaturase/genetics , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Oxidation-Reduction , PPAR alpha/deficiency , Polymerase Chain Reaction/methods , RNA, Messenger/genetics
13.
Anim Genet ; 40(2): 157-64, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19243366

ABSTRACT

Quantitative trait loci (QTL) influencing the weight of abdominal fat (AF) and of breast muscle (BM) were detected on chicken chromosome 5 (GGA5) using two successive F(2) crosses between two divergently selected 'Fat' and 'Lean' INRA broiler lines. Based on these results, the aim of the present study was to identify the number, location and effects of these putative QTL by performing multitrait and multi-QTL analyses of the whole available data set. Data concerned 1186 F(2) offspring produced by 10 F(1) sires and 85 F(1) dams. AF and BM traits were measured on F(2) animals at slaughter, at 8 (first cross) or 9 (second cross) weeks of age. The F(0), F(1) and F(2) birds were genotyped for 11 microsatellite markers evenly spaced along GGA5. Before QTL detection, phenotypes were adjusted for the fixed effects of sex, F(2) design, hatching group within the design, and for body weight as a covariable. Univariate analyses confirmed the QTL segregation for AF and BM on GGA5 in male offspring, but not in female offspring. Analyses of male offspring data using multitrait and linked-QTL models led us to conclude the presence of two QTL on the distal part of GGA5, each controlling one trait. Linked QTL models were applied after correction of phenotypic values for the effects of these distal QTL. Several QTL for AF and BM were then discovered in the central region of GGA5, splitting one large QTL region for AF into several distinct QTL. Neither the 'Fat' nor the 'Lean' line appeared to be fixed for any QTL genotype. These results have important implications for prospective fine mapping studies and for the identification of underlying genes and causal mutations.


Subject(s)
Abdominal Fat/anatomy & histology , Chickens/anatomy & histology , Chickens/genetics , Muscle, Skeletal/anatomy & histology , Animals , Chickens/growth & development , Chromosome Mapping , Female , Genotype , Hybridization, Genetic , Male , Microsatellite Repeats , Multivariate Analysis , Phenotype , Quantitative Trait Loci
14.
Biosystems ; 84(2): 153-74, 2006 May.
Article in English | MEDLINE | ID: mdl-16556482

ABSTRACT

We introduce a mathematical framework that allows to test the compatibility between differential data and knowledge on genetic and metabolic interactions. Within this framework, a behavioral model is represented by a labeled oriented interaction graph; its predictions can be compared to experimental data. The comparison is qualitative and relies on a system of linear qualitative equations derived from the interaction graph. We show how to partially solve the qualitative system, how to identify incompatibilities between the model and the data, and how to detect competitions in the biological processes that are modeled. This approach can be used for the analysis of transcriptomic, metabolic or proteomic data.


Subject(s)
Models, Biological , Oligonucleotide Array Sequence Analysis , Fatty Acids/biosynthesis
15.
Poult Sci ; 82(2): 242-50, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12619801

ABSTRACT

Using two-dimensional (2D)-PAGE, partial protein internal sequencing, and PCR with degenerate primers, we cloned a novel cDNA named HEP21 from hen egg white. The 0.5-kb cDNA encodes a 106 amino acid protein with a cysteine spacing pattern suggesting that HEP21 is a new member of the uPAR/CD59/Ly-6/ snake neurotoxin superfamily. The closest homology of HEP21 is to mouse Ly-6C. Unlike most members of this protein family, HEP21 is not glycosylphosphatidylinositol (GPI)-anchored but is a secreted protein, as indicated by its localization and the presence of a signal peptide in its sequence. Moreover, HEP21 appears as an original member of this protein superfamily because it is predominantly expressed in a tissue, i.e., the oviduct, and especially the magnum where the egg white components are secreted.


Subject(s)
Chickens , Egg Proteins/genetics , Egg Proteins/metabolism , Egg White/analysis , Amino Acid Sequence , Animals , Base Sequence , Cloning, Molecular , DNA, Complementary/analysis , Egg Proteins/chemistry , Electrophoresis, Gel, Two-Dimensional , Female , Gene Expression , Molecular Sequence Data , Oviducts/chemistry , Random Amplified Polymorphic DNA Technique , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, Protein , Sequence Homology
16.
Poult Sci ; 82(1): 54-61, 2003 Jan.
Article in English | MEDLINE | ID: mdl-12580245

ABSTRACT

Sterol regulatory element binding protein-1 and -2 (SREBP-1 and -2) are key transcription factors involved in the biosynthesis of cholesterol and fatty adds. The SREBP have mainly been studied in rodents in which lipogenesis is regulated in both liver and adipose tissue. There is, however, a paucity of information on birds, in which lipogenesis occurs essentially in the liver as in humans. As a prelude to the investigation of the role of SREBP in lipid metabolism regulation in chicken, we sequenced the cDNA, encoding the mature nuclear form of chicken SREBP-2 protein, mapped SREBP-1 and -2 genes and studied their tissue expressions. The predicted chicken SREBP-2 amino acid sequence shows a 77 to 79% identity with human, mouse, and hamster homologues, with a nearly perfect conservation in all the important functional motifs, basic, helix-loop-helix, and leucine zipper (bHLH-Zip) region as well as cleavage sites. As in the human genome, SREBP-1 and SREBP-2 chicken genes are located on two separate chromosomes, respectively microchromosome 14 and macrochromosome 1. Tissue expression data show that SREBP-1 and SREBP-2 are expressed in a wide variety of tissues in chicken. However, unlike SREBP-2, SREBP-1 is expressed preferentially in the liver and uropygial gland, suggesting an important role of SREBP-1 in the regulation of lipogenesis in avian species.


Subject(s)
CCAAT-Enhancer-Binding Proteins/genetics , Chickens/genetics , Chromosome Mapping , Cloning, Molecular , DNA, Complementary/genetics , DNA-Binding Proteins/genetics , Gene Expression , Transcription Factors/genetics , Amino Acid Sequence , Animals , Blotting, Northern , CCAAT-Enhancer-Binding Proteins/chemistry , Cricetinae , DNA-Binding Proteins/chemistry , Humans , Mice , Molecular Sequence Data , Organ Specificity , Polymorphism, Genetic , RNA, Messenger/analysis , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology , Sterol Regulatory Element Binding Protein 1 , Sterol Regulatory Element Binding Protein 2 , Transcription Factors/chemistry
18.
Anim Genet ; 32(5): 289-97, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11683716

ABSTRACT

In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription-polymerase chain reaction (RT-PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo-d(T) reverse-primers and 20-mer arbitrary forward-primers. A purification step by single strand conformation gel electrophoresis was added before sequencing. With a ratio of 112 unique sequences out of 155, we found this method to be highly effective when compared with EST production with randomly selected clones from non-subtracted, non-normalized libraries. A large proportion of the ESTs sequenced correspond to genes involved in transcriptional and post-transcriptional events. Cytogenetic mapping was performed for a subset of ESTs and four regions of conserved synteny between chicken and human were confirmed.


Subject(s)
Chickens/genetics , Expressed Sequence Tags , Animals , Humans , In Situ Hybridization, Fluorescence , Liver/metabolism , RNA/analysis , Reverse Transcriptase Polymerase Chain Reaction , Sequence Alignment , Synteny
19.
Article in English | MEDLINE | ID: mdl-10825667

ABSTRACT

In response to overfeeding, the Landes goose develops a fatty liver that is twice as large as that of the Poland goose, despite similar food intake. The role of hepatic lipogenesis in the genetic susceptibility to fatty liver was assessed in male overfed geese of the two breeds. For a similar hepatic protein content, total activities of malic enzyme, glucose-6-phosphate dehydrogenase, acetyl-Coa-carboxylase and fatty acid synthase, and specific activity and mRNA level of malic enzyme were about two-fold higher in the Landes goose. In the Poland goose, the weight of the fatty liver was correlated positively with the specific activity of ME and the VLDL concentration, which was not the case in the Landes breed. These results show that: (1) hepatic lipogenesis remains very active until the end of the overfeeding period; (2) the pentose-phosphate pathway may function in birds, contrary to what is assumed usually; (3) the level of hepatic lipogenesis is a major factor in the susceptibility to hepatic steatosis in different breeds of geese; and (4) ME activity may be a limiting factor of lipid synthesis in the less susceptible Poland breed.


Subject(s)
Bird Diseases/metabolism , Fatty Liver/veterinary , Geese/metabolism , Liver/metabolism , Acetyl-CoA Carboxylase/metabolism , Animals , Body Composition , Disease Susceptibility , Fatty Acid Synthases/metabolism , Fatty Liver/metabolism , Genetic Predisposition to Disease , Glucosephosphate Dehydrogenase/metabolism , Lipoproteins, VLDL/analysis , Malate Dehydrogenase/metabolism , Male
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