Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Heterozygous F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73xMo17 and Mo17xB73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots early in the developmental manifestation of heterosis. The application of novel and robust statistical approaches and a suitable experimental design established that 35,202 (i.e., 89%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 60% (20,889/35,202) of all expressed genes were differentially expressed between the two parents and 34% to 47% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ~9% of expressed genes exhibited non-additive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis 865 genes were expressed in only one of the two parents, but in both hybrids,. For ~50 genes it was shown that this was a consequence of complementation of PAVs. For several hundred other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids >10% of expressed genes exhibited allelic-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome.

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