Whole genome sequencing of experimental inbred chicken lines using pooled samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51681 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9521750_1.fastq.gz | Fastqsanger.gz | |||
| ERR9521750_2.fastq.gz | Fastqsanger.gz | |||
| ERR9521760_1.fastq.gz | Fastqsanger.gz | |||
| ERR9521760_2.fastq.gz | Fastqsanger.gz | |||
| ERR9521770_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. DNA methylation in the gene body region, especially in the internal exons, was higher than in the 5’ and 3’ flanking regions of genes.Differentially methylated region (DMR) analysis indicated widespread differences between the Leghorn and Fayoumi lines. Of particular interest, many identified DMR-associated genes were significantly enriched in immune-related groups, which indicate that DNA methylation may regulate host immune response to pathogen infection in chickens as these two genetic lines have demonstrated differential resistance to a few pathogens. This work establishes a comprehensive and precise DNA methylation pattern in chickens and lays a solid foundation for future studies on epigenetic modifications related to poultry growth, disease, and development.
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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.
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