Zea mays Transcriptome or Gene expression

The regulation of gene expression is theorized to play an important role in species evolution. The cloning of a few key genes underlying the major morphological changes during maize domestication has highlighted the importance of regulatory differences, however, the global regulatory changes following domestication remain largely unknown. Here, we report a comprehensive assessment of gene expression variation by sequencing the transcriptome of a large maize-teosinte experimental population. We detected evidence for a transcriptome-wide directional shift toward higher expression of maize alleles for genes overall. We showed that genes for secondary metabolism are more likely subject to local regulatory modifications, reflecting the importance of secondary metabolic diversification in plant speciation. We demonstrated that clustered genes for benzoxazinoid biosynthesis are under parallel local regulatory modifications. A number of distant eQTL hotspots were identified, with their targets significantly enriched in specific functional categories. Additionally, we detected a transcriptome-wide reduction in gene expression variability that likely accompanied maize domestication.