Natural variation for gene expression responses to abiotic stress in maize

Amanda J. Waters, Irina Makarevitch, Jaclyn Noshay, Liana T. Burghardt, Candice N. Hirsch, Cory D. Hirsch, Nathan M. Springer

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis- and trans-regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14-day-old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele-specific transcript abundance in the F1 hybrids, we were able to measure the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Although examples of trans-regulatory variation were observed, cis-regulatory variation was more common for both steady-state and stress-responsive expression differences. The genes with cis-allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity.

Original languageEnglish (US)
Pages (from-to)706-717
Number of pages12
JournalPlant Journal
Issue number4
StatePublished - Feb 1 2017

Bibliographical note

Funding Information:
The authors would like to acknowledge the Texas Advanced Computing Center (TACC) at the University of Texas at Austin for computational resources and storage space necessary to complete this project. All of the Illumina sequencing was performed at the University of Minnesota Genomics Center (UMGC). The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. In addition, Peter Hermanson and James Satterlee assisted with sample processing and wet lab techniques. This research was funded by a NSF grant awarded to N.M.S. and I.M. (IOS-1444456). The authors declare no conflict of interest.

Publisher Copyright:
© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd

Copyright 2017 Elsevier B.V., All rights reserved.


  • Zea mays
  • abiotic stress
  • allele-specific expression
  • gene expression
  • regulatory variation

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