Reshaping of the maize transcriptome by domestication

Ruth Swanson-Wagner, Roman Briskine, Robert Schaefer, Matthew B. Hufford, Jeffrey Ross-Ibarra, Chad L Myers, Peter L Tiffin, Nathan M Springer

Research output: Contribution to journalArticlepeer-review

92 Scopus citations

Abstract

Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.

Original languageEnglish (US)
Pages (from-to)11878-11883
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number29
DOIs
StatePublished - Jul 17 2012

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