Genome-wide composite interval mapping (GCIM) of expressional quantitative trait loci in backcross population

Abstract

One of the most remarkable findings in expressional quantitative trait locus (eQTL) mapping is that trans (distal) eQTL has small effect. The widely used approaches have a low power in the detection of small-effect eQTL. To overcome this issue, we integrate polygenic background control with multi-locus genetic model to develop genome-wide composite interval mapping (GCIM). This chapter covers the GCIM procedure in a backcross or doubled haploid populations. We describe the genetic model, parameter estimation, multi-locus genetic model, hypothesis tests, and software. Finally, some issues related to the GCIM method are discussed.