Dissecting The Regulatory Divergence Between Maize And Its Progenitor,teosinte

The regulation of gene expression has been shown to play an important role in controlling organismic phenotypes and species evolution.Here,we report a comprehensive assessment of gene expression variation by sequencing the transcriptome of a large maize-teosinte experimental population.By combiningwith 19,838 SNP markers,eQTL mapping was performed.Major findings are as follows.1.Genome-wide genetic mapping identified 25,660 expression quantitative trait loci(eQTL)for 17,311 genes,including 13,148(51.2%)local-eQTL and 12,512(48.8%)distant-eQTL.Local-eQTL typically had larger effects than distant-eQTL.Of genes with eQTL mapped,76%had local-eQTL.These results suggested that local regulatory effects play a predominant role in determining expression variation of most genes.2.Local-eQTL more frequently mapped to adjacent genes,displaying a mode of expression piggybacking,which consequently created a number of co-regulated gene clusters.Genes within the co-regulated gene clusters tend to have related function and shared chromatin modification.3.Distant-eQTL are not evenly distributed along the maize genome,but form 125 significant distant-eQTL hotspots with their targets significantly enriched in specific functional categories.By integrating different sources of information,we identified putative trans-regulators for a variety of metabolic pathways.4.At Hotspot 30 on chromosome 2,significant distant-eQTL were detected for nine members of the benzoxazinoid metabolic pathway(Bx2-Bx8 and Bx11-Bx12),suggesting that Hotspot 30 might contain a trans-regulator that coordinately regulates the expression of the Bx genes.Through yeast-one-hybrid(Y1H)experiment and transient expression assay,we showed that a R2R3-MYB transcription factor,ZmMYB35,functions as a key regulator that negatively regulates the expression of Bx genes for the biosynthesis of benzoxazinoids.5.We compiled a list of 5,223 genes with local effects that were also detected in the DE or ASE study.At 56%of the local-eQTL mapped for these genes,the maize allele was more highly expressed than the teosinte allele,suggesting that domestication has significantly impacted the global gene expression,with many of genes targeted by selection.6.By integrating expression,genome sequence,and metabolic analyses,we demonstrated that the Bx genes for benzoxazinoid biosynthesis have been coordinately modified for the adaptation of maize to temperate environments with a distinct herbivore community.