Transcriptomic plasticity of maize hybrids and their parental inbred lines at the interface of genotype and development

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Commercial maize production is almost exclusively hybrid-based, because maize hybrids perform significantly better than their homozygous parents. Nevertheless, the molecular basis of this phenomenon, known as heterosis, remains largely enigmatic.In the first funding period we discovered a specific form of complementation of gene expression that we designated single parent expression (SPE). SPE-genes are expressed in only one of the two parental inbred lines but in both reciprocal hybrids. In maize root tissues we discovered >2.300 SPE-genes. As a consequence of SPE, in all root tissues under analysis, the total number of active genes in hybrids exceeded the number of genes expressed in their parental inbred lines by >400. Moreover, non-syntenic genes which emerged only after the last whole genome duplication of maize were significantly overrepresented among SPE genes.In the second funding period, we plan to extend these analyses by surveying the influence of genotype and development on the transcriptomic plasticity of maize hybrids by RNA-Sequencing experiments. The genotype-dependent control of transcriptomic plasticity in maize primary roots will be studied in six crosses of the recurrent female parent B73 with the inbred lines A554, H84, H99, OH43, W64A and Mo17. Developmental control of transcriptomic complexity will be monitored in these genotypes at three developmental stages defined by the length of primary roots. A major focus of the planned experiments will be to further explore the prevalence and role of SPE patterns during the manifestation of heterosis in maize primary roots and the identification of novel genotype specific SPE patterns. Moreover, the evolutionary origin of these genes, teir prevalence among classical maize genes identified by their visible mutant phenotype, their regulation and their function will be surveyed. Furthermore, differential, non-additive and allele-specific gene expression patterns will be determined to identify conserved and unique patterns between these genotype combinations during development. Finally, these expression patterns will be correlated with phenotypic and histological data to gain initial insights into the role of gene expression patterns in the developmental manifestation of heterosis in maize roots. These correlations with a relative small number of genotypes are expected to be relatively weak but might provide first cues for future research directions using larger panels of genotypes.In summary, the analysis of the genotypic and developmental control of the transcriptomic plasticity of maize hybrids and their parental inbred lines will provide insights into the complex molecular processes leading to heterosis manifestation in maize roots.