Chicken Whole Genome Resequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30270 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR2985540.fastq.gz | Fastqsanger.gz | |||
| ERR2985540_1.fastq.gz | Fastqsanger.gz | |||
| ERR2985540_2.fastq.gz | Fastqsanger.gz | |||
| ERR2985550.fastq.gz | Fastqsanger.gz |
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Project description:Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen. Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response. For the test DNA in Fayoumi and Leghorn, samples from 6 inbred Fayoumi and 6 inbred Leghorn individuals were used; For the test DNA in the Campylobacter genetic lines, samples from 24 individual broilers of Line A (in pools of 4) and 24 individual broilers of Line B (in pools of 4) were used. For the reference DNA, Red Jungle Fowl line UCD001 was used from a self-self hybridization.
2016-02-11 | E-GEOD-44440 | biostudies-arrayexpress
Project description:Chicken (Gallus gallus) were first domesticated from a wild form called red jungle fowl that still runs wild in most of southeast Asia. After then the grey jungle fowl (G. sonneratii) was hybridized, which was occurred probably about 8,000 years ago, and domestic chickens have been selected to have ideal economic traits such as a meat and a laying breed. In these breeds, a meat breed such as broiler is the most distributed in poultry industry. In addition, calcium is essential for normal cellular function and blood coagulation. However, it caused the hypocalcemia and the hypercalcemia if calcium intake was less and more than adequate calcium intake such as hypocalcemia and hypercalcemia, which is related to hypertension and blood pressure. So, we generated RNA-seq data from nine chicken broilers according to calcium intake (0.8, 1.0 and 1.2percent) for gene expression profiling. As a result, we identified differentially expressed genes (DEGs) using cufflinks (128 DEGs between 0.8 versus 1.0 percent, 141 DEGs between 0.8 versus 1.2 percent and 103 DEGs between 1.0 versus 1.2 percent), also 12 DEGs were identified by generalized linear model (GLM) within edgeR. We identified that these DEGs were related to hypertension and blood pressure through the KEGG pathway enrichment, the co-occurrence and the protein/protein interaction (PPI) network analysis. In summary, the objective of this study was to investigate the influence of increasing calcium intake in chicken broilers kidney. Therefore, we suggested that higher calcium intake than adequate in chicken broilers can caused the hypertension and high blood pressure.
2017-11-01 | GSE89544 | GEO
Project description:Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other.
2013-12-23 | GSE44394 | GEO
Project description:Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other. In this study, we used affymetrix microarray to profile global gene expression of three distinct genetic lines of chickens to identify functional pathways associated with leanness of domestic chickens.
2013-12-23 | E-GEOD-44394 | biostudies-arrayexpress
Project description:Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen. Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response.
2016-02-11 | GSE44440 | GEO
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations.
2010-04-02 | GSE21169 | GEO
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations.
2010-04-02 | GSE21167 | GEO
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks) by microarray hybridization experiment. Taken together, 543 differentially expressed probe sets were found between broilers and layers across different developmental stages, including genes related to muscle growth and hypertrophy, fatty acid transportation and metabolism, protein degradation, and several important signaling pathways. The expression profiles of a few differentially expressed genes were highly correlated with the growth rates of broilers and layers. We also identified SNPs within upstream transcription factor binding sites of a few differentially expressed genes, indicating that these SNPs might be the causing factor of the expression differences of these genes between broilers and layers. These studies provided new clues for deciphering mechanisms underlining muscle development and organ size control in different chicken lines, will shed light on the study of human muscle related disease as well. Experiment Overall Design: Pectoralis major muscles were sampled from broilers and layers at indicated developmental stage (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks). Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. Affymetrix Gene Chip array hybridization was carried out according to Affymetrix Expression Analysis Technical Manual by GeneTech Biotechnology Limited Company (Shanghai, China). Following labeled cRNA fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45â on Affymetrix Chicken Genome Array. After standard washing and staining, GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
2009-01-14 | E-GEOD-9251 | biostudies-arrayexpress
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks) by microarray hybridization experiment. Taken together, 543 differentially expressed probe sets were found between broilers and layers across different developmental stages, including genes related to muscle growth and hypertrophy, fatty acid transportation and metabolism, protein degradation, and several important signaling pathways. The expression profiles of a few differentially expressed genes were highly correlated with the growth rates of broilers and layers. We also identified SNPs within upstream transcription factor binding sites of a few differentially expressed genes, indicating that these SNPs might be the causing factor of the expression differences of these genes between broilers and layers. These studies provided new clues for deciphering mechanisms underlining muscle development and organ size control in different chicken lines, will shed light on the study of human muscle related disease as well. Keywords: Time-course studies of two different intra-species breeds
2009-01-01 | GSE9251 | GEO
Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740. The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR), and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.
2015-05-14 | E-GEOD-54117 | biostudies-arrayexpress