Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.

ABSTRACT:

Background

Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines.

Results

In Zea mays, the in

SUBMITTER: Zhan S 

PROVIDER: S-EPMC8056621 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature