Why Non-Reciprocal Homoeologous Genetic Exchanges Should be Taken in Account in mRNA-Seq Differential Expression Analysis

Many important crops are allopolyploids; they combine two or more sets of related chromosomes (homeologues), some of them showing evidences of past inter-homeologous exchanges. Among these events, the non-reciprocal homeologous exchanges (NRHEs), are characterized by the loss of a chromosomal region that is replaced by a duplicate copy of the corresponding homeologous region; they could be either be shared between different accessions or be specific to some genotypes.

In this study, we investigate the consequences of NRHEs for mRNA-seq differential expression analysis. After confirming the occurrence of NRHEs events in two representative B. napus accessions, we quantify to what extent these genotype-specific NRHEs impact read mapping and differential expression between these two varieties. Overall, our results indicate that NHREs characterization should be a prerequisite before conducting a differential expression analysis.