Heterosis defines the increased vigor displayed by hybrid progeny compared to the inbred parents. Its molecular basis is not understood, except that genetic differences between parents are the likely cause. This work addresses the hypothesis that "Hybrids suffer regulatory impairment because the parental contribution to regulatory complexes is mismatched in structure or amount. Relaxed regulation results in activation of pathways that cause enhanced growth". To test this hypothesis RNA abundance, allelic contribution, and chromatin state will be investigated using hybrids of rice. The objectives are to: (i) Compare the effect of evolutionary distance on parents-hybrid expression differences and parental expression preference. (ii) Correlate expression changes to promoter activity and changes in repressive chromatin state. (iii) Examine the effects of hybridity on regulatory networks to determine if genes associated with growth are targets of hybrid misregulation. This analysis will entail RNAseq to distinguish parental expression contributions, and will employ a bioinformatic and computational team for dissection of regulatory hierarchies. By exploring a specific hypothesis of heterosis, this work will provide important information on the overall regulatory effect of hybridity. Because the biological system is rice, the best understood grass genome and, globally, the most important food crop, the acquired knowledge is likely to impact both our basic understanding of cellular function and the molecular understanding of pathways that may affect yield in wheat, maize and other critical crops for the US economy. Educational components of this research will involve training of undergraduates from local and from under-represented communities. The GEO expression database, and this laboratory website (RNA-Seq and CHIP-Seq data) will make the data available to the public.
The project is a collaboration between the Comai Laboratory, the Kinoshita Laboratory at NAIST, and the Filkov computational biology group at the UCD department of Computer Science. The Kinoshita laboratory produce RNA and chromatin from hybrids of Oryza sativa subspecies japonica x Oryza sativa subspecies indica, and Oryza sativa subspecies japonica x Oryza punctata. The RNA and chromatin is profiled in the Comai laboratory and analyzed in collaboration with the Filkov group.