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

doi:10.1111/tpj.13414

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

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86 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	706-717
Number of pages	12
Journal	Plant Journal
Volume	89
Issue number	4
DOIs	https://doi.org/10.1111/tpj.13414
State	Published - 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

Keywords

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

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title = "Natural variation for gene expression responses to abiotic stress in maize",

abstract = "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.",

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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: {\textcopyright} 2016 The Authors The Plant Journal {\textcopyright} 2016 John Wiley & Sons Ltd",

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AU - Hirsch, Candice N.

AU - Hirsch, Cory D.

AU - Springer, Nathan M.

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Natural variation for gene expression responses to abiotic stress in maize

Abstract

Bibliographical note

Keywords

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