Transcriptomic and Epigenetic Adaptation of the Maize Chromosome in Oat–Maize Addition Lines. maize,oats

Here, we report the transcriptional and epigenetic adaptation of alien maize chromosomes to oat genomic environment in two oat–maize addition (OMA) lines. Consistent with the stable inheritance of the alien maize chromosome, we found only a very small expansion on the transcriptome size of the maize chromosome and also confirmed that the majority of maize genes recapitulated the maize-specific transcription in the oat genomic environment. Nevertheless, differentially expressed genes (DEGs) were identified, and they represented approximately a quarter of the expressed genes localized in the two maize chromosomes. Notably, by comparing the transcript similarity between the orthologous pairs in oat and maize, we found that the conserved orthologs appeared to be more differentially expressed in OMA lines than the less conserved orthologs. Additionally, both syntenic genes and highly abundant genes were overrepresented among DEGs. Gene suppression was slightly more common than activation among the DEGs. However, the genes in the former maize pericentromere, which expanded to become the new centromere in OMA lines, were activated. Moreover, the three histone modifications (H3K4me3, H3K9ac and H3K27me3) supported transcriptome analysis results consistently.