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Cis and trans-acting eQTL mapping from RNAseq data in swine populations
Mapping eQTL serves an important goal of animal breeders and evolutionary biologists, by elucidating the genetic basis underlying variability in gene expression that ultimately contributes to complex trait phenotypes. In the past, microarrays have been used as the main expression profiling tool, but they are being quickly replaced with RNA sequencing (RNAseq). RNAseq can not only be used to measure total gene expression in eQTL studies, but the technology also offers other advantages. In particular, allelic specific expression (ASE) tests can be used to map cis-acting eQTL. A challenge for implementation of ASE tests involves calling genotypes from data with unbalanced allelic expression. In this paper we show how eQTL analysis from RNAseq data can be performed in outbred livestock populations or their crosses and we illustrate it with results from the MSU F2 pig resource population.
Keywords:
eQTL
allele specific expression
pigs
