Dust samples from turkey flocks
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27886 | ENA |
REPOSITORIES: ENA
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Project description:The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59±0.09, pH[normal] = 5.77±0.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect.
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Project description:Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum Keywords: time course, embryo development Pooled samples from 6 embryos were arraged on a complete interwoven loop design where each treatment (embryonic ages 20, 22, 24, 26 and 28) was replicated 4 times (2 dye-swaps).
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Project description:The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59M-BM-10.09, pH[normal] = 5.77M-BM-10.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect. The mRNA profiles of normal and PSE turkey breast muscle were generated by deep sequencing using Illumina GAIIx platform. Multiplexing was performed (2 samples/lane). Afterwards, difference in gene expression between normal and PSE samples were tested.
2014-01-27 | E-GEOD-37176 | biostudies-arrayexpress
Project description:Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum Keywords: time course, embryo development
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