RT Journal Article SR Electronic T1 A role for heritable transcriptomic variation in maize adaptation to temperate environments JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.01.28.478212 DO 10.1101/2022.01.28.478212 A1 Guangchao Sun A1 Huihui Yu A1 Peng Wang A1 Martha Lopez Guerrero A1 Ravi V. Mural A1 Olivier N. Mizero A1 Marcin Grzybowski A1 Baoxing Song A1 Karin van Dijk A1 Daniel P. Schachtman A1 Chi Zhang A1 James C. Schnable YR 2022 UL http://biorxiv.org/content/early/2022/01/28/2022.01.28.478212.abstract AB Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression. While genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7,614 genes. Rare allele burden within genomic intervals with trans-eQTLs correlated with extremes of expression in target genes as previously reported for cis-eQTLs. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in phytohormone pathways, cell wall biosynthesis, lipid metabolism and stress response. Several genes involved in cell proliferation, flower development, DNA replication and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.Competing Interest StatementJames C. Schnable has equity interests in Data2Bio, LLC; Dryland Genetics LLC; and EnGeniousAg LLC. He is a member of the scientific advisory board of GeneSeek and currently serves as a guest editor for The Plant Cell. The authors declare no other competing interests.