Transcription profiling of pig tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: Miguel Perez-Enciso
PROVIDER: E-GEOD-10898 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues. Are all tissues equally affected by breed or sex? How relevant is tissue in terms of total transcriptome variability? Keywords: breeds, sex and tissues comparison
2008-04-16 | GSE10898 | GEO
Project description:Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development. Experiment Overall Design: Sixteen animals, four from each of four breeds, Large White (LW), Duroc (DU), Youli (YL) and Iberian (IB) piglets were sampled. These breeds represent a wide genetic variability in current pig breeding schemes. There were two males and two females per breed except in Youli, represented by three males and one female. Animals were bought from three breeding companies and transferred to the University experimental farms at weaning, i.e., aged one month approximately. Pigs were housed simultaneously, fed the same diets during the fattening period, that lasted two months, and were weighed at weekly intervals. At the time of slaughter, the average ages were 87, 83, 80 and 89 days for Large White, Duroc, Youli and Iberian pigs, respectively. Their mean live weights at that time were 27.2 (LW), 23.1 (DU), 18.9 (YL) and 17.4 kg (IB). Experiment Overall Design: Animals were euthanized, after 24h fasting, by an overdose of intravenous sodium thiobarbital. At necropsy, tissue samples were collected, snap frozen in liquid nitrogen and stored at -80 ºC. The average time gap between euthanasia and tissue collection was ~ 15 minutes, maximum time was 25 minutes. The tissues collected were hypothalamus (HYPO), adenohypophysis (AHYP), which was separated from the neurohypophysis, thyroid gland (THYG), gonads (GONA) from both sexes, and back fat tissue (FATB). The hypothalamus included the mamillary body and grey tubercle but excluded the chiasma opticum. Throughout this work, each sample was identified by the acronym of the tissue followed by the animal id, e.g., FATBLWF1 refers to back fat tissue from female 1 Large White.
2009-02-21 | E-GEOD-14739 | biostudies-arrayexpress
Project description:Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development.
2009-02-12 | GSE14739 | GEO
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows). To assay for changes in gene expression during piglet maturity, mRNA was isolated from 61 fetal skeletal muscle samples with 8 different conditions: two fetal gestational ages (90 or 110 days of gestation), associated with four genotypes (two extreme breeds for mortality at birth (MS and LW) and two crossed breeds (MSLW and LWMS)). MS fetuses are known to have a better survival at birth than LW fetuses. An understanding of maturity is possible with the comparison between the fetal gestational ages and between the two extreme breeds. The impact of parental genotypes is studied with the presence of crossed fetuses. After quality control and normalization, only 61 samples were conserved (represented here).
2014-09-19 | E-GEOD-56301 | biostudies-arrayexpress
Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism.
2012-05-16 | GSE30343 | GEO
Project description:Custom exome aCGH analysis of copy number across the genomes of 16 canine breeds Two-condition experiment, All breed samples were compared to a single Boxer reference, Seizure samples were compared to breed and sex matched controls, and German Shepherds were compared to the Boxer reference
2012-03-08 | E-GEOD-36333 | biostudies-arrayexpress
Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism. The mRNA expression differences of eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates are measured.
2012-05-15 | E-GEOD-30343 | biostudies-arrayexpress
Project description:The hypothalamus is implicated in controlling feeding and adiposity, besides many other physiological functions, and thus can be of great importance in explaining productive differences between lean and fatty pig breeds. The present study aimed to evaluate the hypothalamic transcriptome of pure Iberian (IBxIB) and Large White x Iberian crossbreds (IBxLW) at 60 days-old, produced in a single maternal environment. Results showed the implication of gender and genotype in the hypothalamic transcriptome, with 51 differentially expressed genes (DEGs) between genotypes and 10 DEGs between genders. Fourteen genotype by sex interactions were found, due to a higher genotype effect on transcriptome found in males. In fact, just 31 DEGs were identified when using only females but 158 using only males. A higher expression of genes related to mitochondrial activity in IBxIB male animals (ND3, ND4, ND5, UQCRC2 and ATP6) was found, which was related to a higher oxidative phosphorylation and greater reactive oxygen species and nitric oxide production. IBxLW male animals showed higher expression of SIRT3 regulator, also related to mitochondrial function. When females were analysed, no such differences were found, since only some differences in genes related to the tricitric acid cycle were observed. Thus, the results indicate a significant effect and interaction of the breed and the sex on the hypothalamic transcriptome at this early age.
2022-04-28 | GSE201408 | GEO
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).
2014-09-19 | GSE56301 | GEO
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).
2017-06-01 | GSE90980 | GEO