Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Targeted genetical genomic to identify genetic mechanisms affecting complex traits: example of meat pH in the chicken

ABSTRACT: Abstract:Genetical genomics has been suggested and proven to be a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfilment of its promise, especially for loci (QTL) of moderate effects. One strategy to overcome the issue is to use a targeted approach: to focus the experiment on one QTL of particular interest. It has two clear advantages: (i) It reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point to investigate downstream effects of the QTL. In the present study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 (12 from each homozygote genotypes at the QTL) were investigated. The targeted QTL was located on chromosome 1 and affected initial pH of meat. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in human. The gene expression study identified ten strong local signals (potentially cis-eQTL) which were markedly more significant compared to the rest of the genome. The differentially expressed genes all mapped to a region < 1 Mb, suggesting a remarkable reduction of the QTL interval compared to the linkage study. These results combined with analysis of downstream effect of the QTL (using gene network analysis) suggest that the QTL is controlling pH by governing oxidative stress. The eQTL results were reproducible with using as few as 4 arrays on pooled samples (with lower significance level). The results demonstrate that this cost effective approach is promising not only for characterization of a QTL also for studying its downstream effects. there are 24 samples from to different genotypes. Each group of genotype has 12 samples. The two groups are compared using a dye balanced design.

ORGANISM(S): Gallus gallus

SUBMITTER: Javad Nadaf

PROVIDER: E-GEOD-47800 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

An expression QTL of closely linked candidate genes affects pH of meat in chickens.

Nadaf Javad J Berri Cecile C Dunn Ian I Godet Estelle E Le Bihan-Duval Elisabeth E De Koning Dirk Jan DJ

Genetics 20140103 3

Genetical genomics has been suggested as a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfillment of its promise, especially for loci (QTL) of moderate effects.One strategy with which to overcome the issue is to use a targeted approach. It has two clear advantages: (i) it reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good s ...[more]

PMID: 24388878

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Dataset Information

Targeted genetical genomic to identify genetic mechanisms affecting complex traits: example of meat pH in the chicken

Publications

An expression QTL of closely linked candidate genes affects pH of meat in chickens.

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