Abstract：Abstract Longping206 (Zea mays), a spreading hybrid in south areas of the Yellow River, Huai and Hai Rivers, with conspicuous growth heterosis and higher yield production, provides us an opportunity to explore the potential molecular mechanism for heterosis. In this study, the new technology Illumina Hiseq2500 was applied to explore the transcription level in sixth leaves stage between Longping206 and its parents (L7221 and L239). Gene expression level and function prediction were analysed with a lot of bioinformatic methods. From the comparison of phenogram, the hybrid was stronger than its paternal line in sixth leaves stage. The measurement of biomass had the same results with the phenogram. After the RNA-Seq sequencing, approximately 12.52 Gb clean data was generated after removing low-quality read. At least 69% read could be mapped into the reference genome of maize B73 with the software Tophat2. With the module Cuffdiff of Cufflinks, gene expression quantity was obtained. Then EBSeq software was used to calculate the differential expression. A total of 3 005 differentially expressed genes (DEGs) was discovered between Longping206 and its parental lines. All 1 788 DEGs were up-regulated in hybrid with 925 DEGs were down-regulated. To calculate the gene expression level in heterosis, traditional quantitative genetic parameters were used as the quantitative traits. To classify the function of DEGs, Gene Ontology (GO) analysis was used. In total, 2 399 of 3 005 DGHP (different expression genes in hybrid and parents) were assigned to at least one term in GO database including molecular function, biological process and cellular component. Most of important biological processes were enriched in hybrid such as hormone signal conditioning, energy metabolism, materials transport, stress threaten etc. To identify the metabolic pathways which the DGHP were involved and enriched, Kyoto Encyclopedia of Genes and Genomes (KEGG) database was performed to analyze the pathway. The results showed that at least 255 DGHP were classified into one functional category. 5.88% and 8.24% of these DEGs were involved in the carbon metabolism and plant signal transduction pathways, respectively. Interestingly, most of the DEGs were up-regulated, which revealed that the two ways were important to the formation of heterosis. qRT-PCR was performed to validate the consistence of transcriptome analysis with 10 random different expression genes. The extensive transcriptome data which was obtained from high-throughput sequencing given the comprehensive overview of the leaf transcriptomes at Longping206 and its parents in a heterotic maize cross. This study provides a useful resource for molecular mechanisms of the maize heterosis research.
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