Treatment- and population-dependent activity patterns of behavioral and expression QTLs

Jesse D. Ziebarth, Melloni N. Cook, Xusheng Wang, Robert Williams, Lu Lu, Yan Cui

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol.

Original languageEnglish (US)
Article numbere31805
JournalPloS one
Volume7
Issue number2
DOIs
StatePublished - Feb 16 2012

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quantitative trait loci
Genes
Gene Expression
Population
Phenotype
Ethanol
Chromosomes
Inbred Strains Mice
Gene expression
Single Nucleotide Polymorphism
genes
Genotype
Genome
phenotype
ethanol
chromosomes
gene expression

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Treatment- and population-dependent activity patterns of behavioral and expression QTLs. / Ziebarth, Jesse D.; Cook, Melloni N.; Wang, Xusheng; Williams, Robert; Lu, Lu; Cui, Yan.

In: PloS one, Vol. 7, No. 2, e31805, 16.02.2012.

Research output: Contribution to journalArticle

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