Zea mays strain:B73, Mo17 and IBM RIL population Transcriptome or Gene expression
Identifiers: SRA: SRP017111
Gene transcription is an essential step of gene function and transcriptome variation is of agronomical, ecological and evolutionary importance. To explore global expression patterns and dissect the underlying genetic mechanisms are important scientific inquires which are still largely unknown, especially between a segregating population and the parents. In our study, we used RNA-Seq to profile the shoot apex transcriptome variation (including protein coding genes and non-coding genes) in maize IBM RIL population, to map eQTLs underlying the transcriptome variations and to utilize eQTLs to clone genes involved in maize shoot apices development. We revealed that: Much of the variation (the population mean, the coefficient of variation) of gene expression levels in RILs is reflective of differences present among the parents; These transcriptome variations could be explained by 30,774 eQTLs with 96 trans-eQTL hotspots; In many cases, the genes commonly regulated by a trans-eQTL hotspot are enriched for a specific function or act in the same genetic pathway; Structural variation within and near genes contributs to cis-regulatory variation. All of these results indicate Mendelian factors play as major contributors to the transcriptome variation. Meanwhile, non-Mendelian regulations were also observed as paramutation-like expression pattern for 145 genes, of which 88% genes were predicted to be potential targets of miRNAs or ta-siRNAs, and as unexpected presence/absence expression patterns for 210 genes. These genes with unexpected presence/absence expression patterns in the RILs likely include examples of functional genes as well as transposed gene fragments that may contribute to regulatory variation of their ancestral syntenic genes.