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. Analysis of allele-specific gene expression (ASE) allows to differentiate between cis- and trans-acting genetic variation. This study was conducted to determine 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. Overall, 19744 genes with identified SNP were found. A special case are single-parent expressed genes (SPE), whose expression could only be detected in one parent. About 9% of all expressed genes were detected as SPE both in control and drought conditions. A gene was considered as cis-regulated if the proportion of the B73 allele in B73 SPE genes or the Mo17 allele in Mo17 SPE genes was ≥90%. For all hybrids and conditions, about 17% of the SPE genes showed cis-acting regulation.