Heterosis or hybrid vigor is a phenomenon in which the F1 progeny is superior in characteristics than its inbred parents. Inbreeding depression refers to the reduced vigor in the offspring from matings involving related parents. The world's most important grain crop, Zea mays exhibits significant heterosis and inbreeding depression, and despite billions of dollars of sales and investments in hybrid maize, the underlying molecular and genetic mechanisms responsible for inbreeding depression and heterosis still remain unknown. We used next generation sequencing technologies and a sample of the most elite publicly available germplasm to explore the role of gene expression in hybrids vs. inbreds. A comparison of transcript counts from inbred parents and their hybrids revealed additive gene action to be the most prevalent among differentially expressed genes. Gene expression that deviated from additivity showed high parent dominance, suggesting that the alleles from the high parent affected the expression in the hybrid more than the alleles from the low parent. Most differentially expressed genes were inconsistent among families, however at a higher level of organization these sets of genes belonged to the same metabolic pathways and were up-regulated in different parents and hybrids, indicating that organisms often utilize compensatory/complementary genetic networks to perform the same task. Allele-specific expression analysis for all inbred-hybrid combinations showed that a majority of alleles that were preferentially expressed in the hybrids also were expressed differentially between its inbred parents. Cis-trans statistical tests revealed that although most alleles exhibit conserved expression, cis-regulation was found to affect alleles more than trans-regulation. Cis regulation was found to be strongly correlated with additive gene action identified from the transcript expression study. In order to explain lowered protein metabolism seen in hybrids, we developed novel software pipelines to investigate alternative splicing patterns in inbreds and hybrids. Results showed that the hybrid preferentially produces parental splice forms, but for a small fraction of genes, the hybrids produce splice forms that are not observed in the parental set. We also found 88% of the genes expressed just a single isoform, while other isoforms are expressed trivially. The exact reason for preferential expression of a single isoform remains to be determined, we hypothesize that the protein structure coded by the most prevalent splice isoform is the most stable.

A direct extension of our work can help identify mis-folded proteins in the hybrids and the alleles that code them and eliminate these alleles through breeding strategies.