A Robust Methodology for Assessing Homoeolog-Specific Expression

Abstract

Angiosperm evolution is marked by numerous, recurring polyploidization events. While hybridization and polyploidization have greatly increased the degree of genetic and phenotypic diversity in plants, the mechanisms underlying changes in the genotype-to-phenotype relationships remain unclear. As the field of natural sciences continues to expand during the post-genomic era, large datasets are becoming increasingly common. However, the development of tools and workflows available to robustly assess these changes have lagged behind data production. A robust homoeolog-specific expression analysis strongly depends upon proper homoeolog calling, the ability to account for reference sequence biases, flexible and accurate methods for dealing with residual bias, and a reproducible workflow. To that end, this chapter aims to provide a detailed description of the potential pitfalls encountered while estimating homoeolog-specific expression as well as provide a workflow that allows for robust inferences based on precise estimates of expression changes.

Keywords: Bayesian inference; Homoeolog; Homoeolog-specific expression; Polyploid; Reference bias.