Gene expression regulation plays an important role in controlling plant phenotypes and adaptation.Here,we report a comprehensive assessment of gene expression variation through the transcriptome analyses of a large maize-teosinte experimental population.Genome-wide mapping identified 25 660 expression quantitative trait loci (eQTL) for 17 311 genes,capturing an unprecedented range of expression variation.We found that local eQTL were more frequently mapped to adjacent genes,displaying a mode of expression piggybacking,which consequently created co-regulated gene clusters.Genes within the co-regulated gene clusters tend to have relevant functions and shared chromatin modifications.Distant eQTL formed 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.We demonstrated that the bHLH transcription factor R1 and hexokinase HEX9 might act as crucial regulators for flavonoid biosynthesis and glycolysis,respectively.Moreover,we showed that domestication or improvement has significantly affected global gene expression,with many genes targeted by selection.Of particular interest,the Bx genes for benzoxazinoid biosynthesis may have undergone coordinated cis-regulatory divergence between maize and teosinte,and a transposon insertion that inactivates Bx12 was under strong selection as maize spread into temperate environments with a distinct herbivore community.

To optimize fitness,plants must efficiently allocate their resources between growth and defense.Although phytohormone crosstalk has emerged as a major player in balancing growth and defense,the genetic basis by which plants manage this balance remains elusive.We previously identified a quantitative diseaseresistance locus,qRfg2,in maize (Zea mays) that protects against the fungal disease Gibberella stalk rot.Here,through map-based cloning,we demonstrate that the causal gene at qRfg2 is ZmAuxRP1,which encodes a plastid stroma-localized auxin-regulated protein.ZmAuxRP1 responded quickly to pathogen challenge with a rapid yet transient reduction in expression that led to arrested root growth but enhanced resistance to Gibberella stalk rot and Fusarium ear rot.ZmAuxRP1 was shown to promote the biosynthesis of indole-3-acetic acid (IAA),while suppressing the formation of benzoxazinoid defense compounds.ZmAuxRP1 presumably acts as a resource regulator modulating indole-3-glycerol phosphate and/or indole flux at the branch point between the IAA and benzoxazinoid biosynthetic pathways.The concerted interplay between IAA and benzoxazinoids can regulate the growth-defense balance in a timely and efficient manner to optimize plant fitness.

Both herbivory and jasmonic acid (JA) activate the biosynthesis of defensive metabolites in maize, but the mechanism underlying this remains un-clear. We generated maize mutants in which ZmMYC2a and ZmMYC2b, two transcription factor genes important in JA signaling, were individually or both knocked out. Genetic and bi-ochemical analyses were used to elucidate the functions of ZmMYC2 proteins in the maize re-sponse to simulated herbivory and JA. Compared with the wild-type (WT) maize, the double mutant myc2ab was highly susceptible to insects, and the levels of benzoxazinoids and volatile terpenes, and the levels of their biosynthesis gene tran-scripts, were much lower in the mutants than in the WT maize after simulated insect feeding or JA treatment. Moreover, ZmMYC2a and ZmMYC2b played a redundant role in maize resistance to insects and JA signaling. Transcriptome and Cleavage Under Targets and Tagmentation-Sequencing (CUT&Tag-Seq) analysis indicated that ZmMYC2s physically targeted 60％of the JA-responsive genes, even though only 33％of these genes were transcriptionally ZmMYC2-dependent. Importantly, CUT&Tag-Seq and dual luciferase assays revealed that ZmMYC2s transactivate the benzoxazinoid and volatile terpene biosynthesis genes IGPS1/3, BX10/11/12/14, and TPS10/2/3/4/5/8 by directly binding to their promoters. Fur-thermore, several transcription factors physically targeted by ZmMYC2s were identified, and these are likely to function in the regulation of benzoxazinoid biosynthesis. This work reveals the transcriptional regulatory landscapes of both JA signaling and ZmMYC2s in maize and provides comprehensive mechanistic insight into how JA signaling modulates defenses in maize responses to herbivory through ZmMYC2s.