Long reads facilitate testing of allele specific expression and estimation of cis- and trans-variance in QTL regions
Authors: Patricka Williams-Simon 1; Adalena Nanni 2,3; Alison Morse 2,3; Hayes Oken 1; Camille Oster 4; Elizabeth King 4; Paul Schmidt 1; Lauren McIntyre 2,3
Affiliations: 1) Department of Biology, University of Pennsylvania, Philadelphia, PA; 2) Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL; 3) University of Florida Genetics Institute, University of Florida, Gainesville, FL; 4) Division of Biological Sciences, University of Missouri, Columbia, MO
Keywords: Complex traits
A combination of quantitative trait locus (QTL) mapping and allele specific expression analysis was developed and used to identify candidate genes for thermo-tolerance, a quantitative trait, in Drosophila melanogaster. QTL analyses for this trait identified intervals containing genes associated with the trait. Four RIL lines (2 high and 2 low) were selected and crossed to a tester line to assay allele specific expression. We used long reads (Oxford Nanopore) to quantify expression in the F1 and identified loci with allele specific expression. Long reads are highly efficient with more than 70% discrimination between alleles in the same species with very little pre-processing needed as errors in the reads do not affect allele assignment in most cases. We compared allele imbalance (AI) between the two high lines and between the two low lines within the QTL region. Inside the QTL the alleles are shared between the two high lines (low lines) and similar AI indicates a shared cis-regulatory effect, as expected based on the QTL. If the two lines with the same QTL allele differ in AI this indicates the presence of a trans-regulatory factor that differs in the two lines. In addition to the analyses within the QTL, the remainder of the genome can be explored for cis, and cis by trans interactions in AI by grouping alleles using marker loci.