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PubMed2026

The current and future perspective of ChickenGTEx project and its applications in precision breeding.

The Chicken Genotype-Tissue Expression (ChickenGTEx) project was established to systematically characterize the regulatory landscape of the chicken genome and to accelerate the translation of functional genomics into precision breeding. By integrating whole-genome sequencing with multi-tissue transcriptomic profiling, ChickenGTEx provides a comprehensive atlas of gene expression regulation across diverse tissues and physiological systems. Current findings demonstrate that complex production traits are governed by coordinated regulatory networks rather than isolated loci, with substantial contributions from tissue-specific gene expression, structural variation, and genotype-by-sex interactions. Sex-dependent regulatory effects further refine the genetic architecture of metabolic, immune, and reproductive traits, highlighting the importance of incorporating sex as a biological variable in genomic analyses. Application of integrative omics frameworks within elite layer populations has revealed multilayer regulatory mechanisms underlying extended laying performance, feed efficiency, metabolic health, and eggshell quality. By partitioning phenotypic variance into genetic, regulatory, and host-microbiome components, these approaches move beyond association-based mapping toward causal inference and biological interpretation. Importantly, validated regulatory loci identified through ChickenGTEx and related analyses provide actionable markers for genomic selection and rational targets for precision genome modification. Looking forward, continued expansion of regulatory atlases, incorporation of single-cell and longitudinal data in diverse environmental conditions, and integration of functional annotation into breeding pipelines will further enhance prediction accuracy and sustainable genetic improvement. The ChickenGTEx project thus represents a foundational platform bridging functional genomics and practical poultry breeding.

Animals↗
PubMed2006

A strategy to search for common obesity and type 2 diabetes genes.

Worldwide, the incidence of type 2 diabetes is rising rapidly, mainly because of the increase in the incidence of obesity, which is an important risk factor for this condition. Both obesity and type 2 diabetes are complex genetic traits but they also share some nongenetic risk factors. Hence, it is tempting to speculate that the susceptibility to type 2 diabetes and obesity might also partly be due to shared genes. By comparing all of the published genome scans for type 2 diabetes and obesity, five overlapping chromosomal regions for both diseases (encompassing 612 candidate genes) have been identified. By analysing these five susceptibility loci for type 2 diabetes and obesity, using six freely available bioinformatics tools for disease gene identification, 27 functional candidate genes have been pinpointed that are involved in eating behaviour, metabolism and inflammation. These genes might reveal a molecular link between the two disorders.

Animals↗
PubMed2000

Polymorphisms in dopamine receptors: what do they tell us?

Many genetic studies have focussed on dopamine receptors and their relationship to neuropsychiatric disease. Schizophrenia, bipolar disorder, and substance abuse have been the most studied, but no conclusive linkage or association has been found. The possible influence of dopamine receptor variants on drug response has not received as much attention. While there is some evidence that polymorphisms and mutations in dopamine receptors can alter functional activity and pharmacological profiles, no conclusive data link these gene variants to drug response or disease. The lack of unequivocal findings may be related, in part, to the subtle changes in receptor pharmacology that these polymorphisms and mutations mediate. These subtle effects may be obscured by the influence of genes controlling drug metabolism and kinetics. Further insight into the pharmacogenetics of dopamine receptors may require not just more studies, but novel approaches to the study of complex genetic traits and diseases.

Animals↗
PubMed1985

Cross-species gene transfer; implications for a new theory of evolution.

It has been established that genes can be transferred and expressed among procaryotes of different species. I am hypothesizing--and there is mounting evidence for this conclusion--that genes are transferred and expressed among all species, and that such exchange is facilitated by, and can help account for, the existence of the biological unities, from the uniform genetic code to the cross-species similarity of the stages of embryological development. If this idea is correct, the uniformity of the genetic code would allow organisms to decipher and use genes transposed from chromosomes of foreign species, and the shared sequence of embryological development within each phylum would allow the organism to integrate these genes, particularly when the genes affect complex morphological traits. The cross-species gene transfer model could help explain many observations which have puzzled evolutionists, such as rapid bursts in evolution and the widespread occurrence of parallelism in the fossil record.

Animals↗
PubMed2004

Present status of genetic mechanisms in hypertension.

Studies on Mendelian hypertension have provided great insight into mechanisms causing hypertension. Mineralocorticoid synthesis and degradation, the mineralocorticoid receptor, sodium channel resorptive mechanisms, and regulation of the thiazide-sensitive sodium-chloride cotransporter have been shown to cause hypertension. Aberrant regulation of peripheral vascular resistance and circulatory regulation have not yet been proved but have been strongly implicated in Mendelian hypertension with brachydactyly. Hypertension as a complex genetic trait has proved more difficult because many genes are involved and the genes have much smaller effects. Association studies, linkage analyses, single nucleotide polymorphism analyses, synteny in animal models, and gene expression studies are the current tools and steady progress is being made.

Humans↗
PubMed2003

Essential hypertension.

Hypertension is a frequent, chronic, age-related disorder, which often entails debilitating cardiovascular and renal complications. Blood pressure is usually noted in combination with other cardiovascular risk factors. Diagnosis of hypertension increasingly relies on automated techniques of blood pressure measurement. The pathophysiology of essential hypertension depends on the primary or secondary inability of the kidney to excrete sodium at a normal blood pressure. The central nervous system, endocrine factors, the large arteries, and the microcirculation also have roles in the disorder. Although monogenic forms of blood pressure dysregulation exist, hypertension mostly arises as a complex quantitative trait that is affected by varying combinations of genetic and environmental factors. Non-pharmacological strategies can reduce blood pressure. Antihypertensive drug treatment diminishes the complications of hypertension. The concept that a few major genes will provide the final clue to the pathogenesis of essential hypertension is an oversimplification that contradicts the heterogeneous nature of this disorder. Further integration of genetic, molecular, clinical, and epidemiological research could disclose subsets of patients in whom specific combinations of genetic and environmental factors raise blood pressure, and might lead to more individualised treatment.

Adolescent↗
PubMed2004

Investigation of completed suicide and genes involved in cholesterol metabolism.

BACKGROUND: Several lines of evidence support the association between low or lowered levels of serum total cholesterol and suicide. Genetic epidemiological studies suggest that genes predispose to suicide. Given that genes control many aspects of cholesterol biosynthesis and metabolism, one approach through which to explore the putative association between low cholesterol and suicide is through genetic studies. METHODS: We examined the potential role of five genes encoding proteins involved in cholesterol biosynthesis and transport in a total sample of 305 male Caucasian subjects, consisting of 145 suicide completers and 160 controls. We investigated variation in the HMG CoA reductase (HMGCR), 7-dehydrocholesterol reductase (DHCR7), lipoprotein lipase (LPL), low-density lipoprotein receptor (LDLR), and apolipoprotein E (APOE) genes. RESULTS: We were unable to detect significant differences in allele or genotype frequencies between the suicide cases and controls for any of the genes studied. No relationship was found between genotype and impulsivity or aggression as measured using the BIS and BDHI, respectively. LIMITATIONS: The limitations of this study are consistent with the typical limitations inherent in most genetic association studies involving complex behavioral traits. CONCLUSION: Although these genes are unlikely to play a major role in susceptibility to suicide, further studies in a larger sample are necessary to reveal the smaller genetic effects, if present.

Adult↗
PubMed1997

Polygenic control of experimental allergic encephalomyelitis in Biozzi ABH and BALB/c mice.

Experimental allergic encephalomyelitis (EAE) is a chronic inflammatory disease of the central nervous system (CNS), with many similarities to multiple sclerosis (MS). Susceptibility to EAE is under genetic control of both the major histocompatibility complex (MHC) and unknown non-MHC gene products. This study uses a selective cross between EAE-susceptible ABH and low responder BALB/c mice, where disease is dominant and affects female mice significantly more than males. In a genome screen using microsatellite markers, linkage analysis suggests that genes encoded on chromosomes 4, 8, 10, 11, 12 and 17 contribute to the development of EAE (p < 0.05), although none of these putative EAE loci fulfilled the criteria for significant linkage. Interestingly, genotype frequency showed significant deviation from the expected random distribution of alleles on chromosomes 4, 8 and 17, (p < 0.001), with 32% of mice developing disease, exhibiting all 3 alleles (p < 0.001). This may indicate complex interactions amongst gene products in the EAE phenotype. This and other recent studies in different mouse strains underlies that EAE is a complex polygenic trait and may provide clues to the genetic mechanisms involved in autoimmune diseases such as multiple sclerosis.

Animals↗
PubMed2002

Evaluation of Lewis and SHR rat strains as a genetic model for the study of anxiety and pain.

The study of inbred strains of rodents that differ for specific behaviours can help us to understand the biological mechanisms underlying complex psychological traits. Lewis (LEW) and SHR inbred rat strains, for example, have been recently proposed as a genetic model for the study of anxiety. Our goal was to characterise two Brazilian substrains of LEW and SHR rats, that have never been compared before, behaviourally and/or pharmacologically, in order to evaluate their potential contribution to studies on anxiety and pain. Male and female LEW and SHR rats were submitted after 8 weeks of age to five anxiety/emotionality tests: the open field (7 or 260 lux), the elevated plus-maze, the elevated T-maze and the black/white box. Rats of all groups were also submitted to the formalin test of nociception and measurement of blood pressure. Significant strain differences (P<0.05) were observed in both sexes for all indices of anxiety and also for measures of pain and blood pressure. SHRs, compared with LEWs, explored more the aversive environments of all anxiety tests, showed less nociceptive responses and were hypertensive. All differences in experimental anxiety parameters agree with previous differences reported between two French LEW and SHR substrains, suggesting that LEWs are more anxious than SHRs, thus consolidating these strains as a useful genetic model for the study of anxiety and pain. The possible involvement of tachykinergic mechanisms is discussed.

Animals↗
PubMed2002

Association analysis of candidate genes for neuropsychiatric disease: the perpetual campaign.

Association studies have been proposed to identify the genetic determinants of complex neuropsychiatric traits. Although such studies of candidate genes offer great potential to identify genetic variants that contribute to the expression of psychiatric disease, no consistent associations have been identified. Studies to date have focused on candidate genes that are selected for analysis on the basis of incomplete information about gene function in the brain, therefore the majority of genes expressed in the brain have been ignored. Additionally, most genetic determinants of psychiatric disease will probably be of modest effect and therefore require association studies of large samples. As genomic technologies advance, massive genotyping of large samples should allow identification of alleles that contribute to psychopathology.

Data Interpretation, Statistical↗
PubMed2000

Increased protein levels of serotonin transporter in frontal cortex of patients with Down syndrome.

Serotonin transporters (SERTs) are presynaptic proteins specialized for the clearance of serotonin from the synaptic cleft. A large body of evidence exists on altered platelet serotonin uptake and metabolism in Down syndrome (DS). Besides, dysregulation of SERTs expression have been reported in various complex behavioural traits and disorders including, neurodegenerative disorders. This prompted us to investigate SERT protein levels in adult brain specimens. Western blot analyses were performed in frontal cortex and cerebellum of aged controls and patients with DS and Alzheimer's disease (AD). The result revealed that frontal cortex SERT was significantly increased (P<0.05) in DS, whereas in AD it was comparable to controls. In cerebellum, no significant difference was observed among the study populations. A remarkable difference was noted when SERT was normalized vs. neuron specific enolase (NSE), a neuronal marker. The increase in SERT/NSE was highly significant (P<0.01) in DS frontal cortex compared to controls. Neither AD frontal cortex nor DS and AD cerebellum did show any significant difference. These findings indicate that a region specific alteration in SERT expression may exist in DS with AD-like pathology. As little is known about the status of serotenergic synaptic markers in DS brain, the findings may contribute to an effort made to delineate the underlying causes of serotonergic dysfunction in DS and the quest for therapeutic strategies. The study also suggest caution should be taken in applying data obtained from DS to model AD biochemical defects.

Adult↗
PubMed1998

Closing in on genes for manic-depressive illness and schizophrenia.

Advances in the human genetic map, and in genetic analysis of linkage and association in complex inheritance traits, have led to genetic progress in the major psychoses. For chromosome 6 in schizophrenia, and chromosomes 18 and 21 in manic-depressive illness, there are reports of linkage in several independent data sets. These are small effect genes, best detected with affected-relative-pair linkage methods. Association with candidate genes is an alternative strategy to uncovering susceptibility genes for these illnesses, but convincing associations remain to be demonstrated. New clinical and laboratory investigation methods are being developed. Testing every gene in the human genome for association with illness has recently been proposed (Risch and Merikangas 1996). This would require further progress in characterizing the genome and in automated large-scale genotyping. The best type of pedigree sampling for common disease studies, whether for linkage or association, is not yet established. An endophenotype hybrid strategy can combine genetic linkage, association, and pathophysiologic studies. As clinical molecular investigation methods advance, identification of disease susceptibility mutations and delineation of their pathophysiological roles may be expected.

Bipolar Disorder↗
PubMed2003

beta-Adducin polymorphisms, blood pressure, and sodium excretion in three European populations.

The associations of the beta-adducin C1797T polymorphism with blood pressure (BP) and various indexes of sodium homeostasis were investigated in 388 men and 456 women, aged 18 to 60 years, recruited from three European populations (Cracow, Poland, n = 300; Novosibirsk, Russian Federation, n = 274; Mirano, Italy; n = 270). Phenotypes included 24-h ambulatory BP and urinary excretion of electrolytes and aldosterone. Subjects were genotyped for the beta-adducin polymorphism. Both a population-based association study and a family-based analysis were performed. Urinary sodium excretion was higher in Cracow than in Mirano (241 v 185 mmol/24 h, P <.05) and intermediate in Novosibirsk (206 mmol/24 h). The beta-adducin T allele (15.2% v 9.1%, P <.0001) was more prevalent in Mirano than in the two Slavic centers. In both population-based and family-based association analyses, there was significant heterogeneity between Slavic and Italian subjects in the phenotype-genotype relationships with beta-adducin. In the Slavic centers, 24-h systolic BP was higher in T allele carriers than in CC homozygotes (122.3 v 119.7 mm Hg, P =.03), whereas this was not the case in Mirano (121.8 v 122.9 mm Hg, P =.42). In Slavic (212.6 v 233.1 mmol/24 h) as well as in Italian (166.1 v 191.5 mmol/24 h) participants, 24-h sodium excretion was lower (P =.01) in T allele carriers than in CC homozygotes. These results were confirmed in the family-based analysis of offspring using a quantitative transmission disequilibrium test. In conclusion, the frequency of the beta-adducin T allele and salt intake differ across European populations. Thus, both variation in genetic background and salt intake may explain the observed heterogeneity in the phenotype-genotype relationships. Genetic determinants of complex quantitative traits such as BP can only be investigated within their epidemiologic context.

Adolescent↗
PubMed1999

Telomeres and essential hypertension.

The dynamics of telomere attrition in human beings might shape the course of age-dependent, complex genetic traits. One of these traits is essential hypertension. Age-dependent telomere attrition could lead to critically shortened telomeres and aneuploidy (ie, the loss or gain of chromosomes) with a resultant mosaicism that will be variably expressed in different cells and tissues. The chromosomal instability and loss of heterozygosity resulting from this process would promote an age-dependent expression of variant genes that harbor susceptibility for essential hypertension or genes that accelerate the process of aging.

Age Factors↗
PubMed1996

Etiology of cancer in humans and animals.

Cancer is a multistep disease with a multifactorial aetiology. Among the avoidable causes of human cancer are exposure to environmental carcinogens, ionizing and non-ionizing radiation, chronic inflammatory states (viruses and parasites) and life style factors, in particular diet. There is increasing evidence that these aetiologic factors may interact with each other resulting in a more than additive cancer risk. This has been demonstrated for example with hepatitis B virus and aflatoxins in hepatocellular carcinoma and alcohol and tobacco in cancer of the esophagus. The integration of molecular markers of exposure, biological effect and individual susceptibility into epidemiological studies can contribute to strengthening the causal link between exposure and disease and thus help assess the relative contribution of multiple risk factors to the aetiology of a specific cancer. For some genotoxic carcinogens the sequence of events leading to tumour formation is well understood from exposure, to metabolism and ultimately to specific mutations in transformation-associated genes. The mechanisms of action of carcinogens which do not interact directly with DNA but exert adverse effects through receptor-mediated modulation of intercellular signal pathways is far less well understood and an example of this is the interaction between diet and hormones. Furthermore, there is increasing awareness that individual response to environmental agents may depend to a significant extent on the genetic background of the individual or population. This has long been known from animal experiments but human cancer susceptibility is a complex genetic trait involving genes responsible for carcinogen metabolism, DNA repair and as yet unidentified cell specific susceptibility genes. Phenotypic changes observed during tumour progression reflect the sequential acquisition of genetic alterations. To assess the contribution of mutations in the various genes involved in the carcinogenic process may require their expression in transgenic animals or knock out mice. This has again placed animal experimentation into the forefront of mainstream cancer research.

Animals↗
PubMed1996

Genetic basis of systemic lupus erythematosus.

Recent studies have emphasized that systemic lupus erythematosus is a complex genetic trait with contributions from the MHC and multiple non-MHC genes. Genome-wide linkage studies in murine models of lupus have mapped the positions of a number of non-MHC loci, but the contributing genes have not yet been identified. Recent studies in human systemic lupus erythematosus have found an association with a particular FCGR2A allele. Although susceptibility genes in lupus are unlikely to involve mutations with severe functional consequences, murine knockout models that develop lupus-like features may provide insight into the pathogenetic mechanisms and contributing genes in the human disease.

Animals↗
PubMed2002

Seed dormancy and germination.

Seed dormancy and germination are complex adaptive traits of higher plants that are influenced by a large number of genes and environmental factors. Studies of genetics and physiology have shown the important roles of the plant hormones abscisic acid and gibberellin in the regulation of dormancy and germination. More recently, the use of quantitative genetics and mutant approaches has allowed the further genetic dissection of these traits and the identification of previously unknown components. Molecular techniques, and especially expression studies and transcriptome and proteome analyses, are novel tools for the analysis of seed dormancy and germination. These tools preferentially use Arabidopsis thaliana because of the molecular genetic resources available for this species. However, Solanaceae and cereals also provide important models for dormancy research.

Arabidopsis↗
PubMed2002

Finding genes for bipolar disorder in the functional genomics era: from convergent functional genomics to phenomics and back.

Psychiatric genetics, while promising to unravel the mechanisms of psychiatric disorders, has proven to be a challenging field. Psychiatric disorders, like other common genetic traits, are complex and heterogeneous. Psychiatric genetics has also suffered from a lack of quantifiable, biology-based phenotypes. However, the field is currently at an opportune moment. The work of various investigators is on the verge of paying rich dividends. Efforts at positional cloning are being greatly accelerated by the fruits of the Human Genome Project. New tools of functional genomics, such as expression profiling and proteomics, are being applied to animal models. These two methods can complement each other in an approach we have termed convergent functional genomics. Lastly, improvements in the measurement of biologically distinct endophenotypes--or phenomic--will lead to a better understanding of the mapping of genes to phenotypes in both animal and human systems.

Journal Article↗