Transcriptomic Analysis of the Highly Heterotic Maize Hybrid Zhengdan 958 and Its Parents During Spikelet and Floscule Differentiation

Heterosis plays an important role in crop production and plant evolution. Although heterosis has been widely exploited by plant breeders, the underlying molecular mechanisms are not well understood. We analyzed gene expression of the highly heterotic maize hybrid Zhengdan 958 and its parents, Zheng 58 and Chang 7-2 during spikelet and floscule differentiation using the GeneChipβ Maize Genome Array. Pairwise comparison among Zhengdan 958 and its parents at the two stages of immature ear development identfied 1 089 and 1 352 differentially expressed genes. Gene ontology (GO) functional analysis showed that these genes participate in many functional categories, and those encoding response to stress and transcription factor may play important roles in heterosis. Pathway analysis showed that the differentially expressed genes are involved in various metabolic processes, and those participating in lipid metabolism, signal transduction, transport, and catabolism may contribute to heterosis. A non-additive expression pattern was prevalent in genes that were differentially expressed between the hybrid and its parents during both spikelet and floscule differentiation. Because genes that are differentially expressed in a hybrid and its parents could underlie heterosis, nonadditive expression patterns might contribute to the manifestation of heterosis.