Allele-Specific Expression in Zea mays Hybrids

Heterosis results in superior heterozygous F1-hybrids compared to their homozygous parental inbred lines. This effect is often associated with gene expression variation between hybrids and parents. We determined allele-specific gene expression (ASE) in reciprocal Zea mays hybrids in comparison with their parental inbred lines in two conditions (control, drought) using four replicates per genotype and condition. Raw reads originating from Zea mays parental inbred lines B73 and Mo17 and their reciprocal heterozygous hybrids were mapped against the B73 reference genome. The aligned reads were inspected for SNPs between B73 and Mo17 and we found 14065 genes with identified SNPs. Of special interest are single-parent expressed genes (SPE), whose expression could only be detected in one parent. About 6% of all expressed genes show this pattern. Only a small proportion could be explained by putative presence-absence-variation between the parental genomes. The majority of SPE genes show expression from both alleles in the hybrid, signifying trans-regulation by a transcriptional activator present in only one parental genome. On the other hand, we identified about 7% of the SPE genes as cis-regulated.