Genome-wide analysis of transcriptional variability in a large maize-teosinte population

Wang, X., Chen, Q., Wu, Y., Lemmon, Z. H., Xu, G., Huang, C., Liang, Y., Xu, D., Li, D., Doebley, J. F., Tian, F. (March 2018) Genome-wide analysis of transcriptional variability in a large maize-teosinte population. Mol Plant, 11 (3). pp. 443-459. ISSN 1674-2052

DOI: 10.1016/j.molp.2017.12.011


The regulation of gene expression plays an important role in controlling plant phenotypes and adaptation. Here, we report a comprehensive assessment of gene expression variation by sequencing the transcriptome 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 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 related function and shared chromatin modification. 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. Finally, we showed that domestication or improvement has significantly impacted 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. We further demonstrated that a transposon insertion that inactivates Bx12 was under strong selection as maize spread into temperate environments with a distinct herbivore community.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
organism description > plant > maize
Investigative techniques and equipment > assays > genome wide association studies
CSHL Authors:
Communities: CSHL labs > Lippman lab
Depositing User: Matt Covey
Date: 5 March 2018
Date Deposited: 10 Jan 2018 15:47
Last Modified: 05 Apr 2018 16:16
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