Journal Articles

RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean

June 04, 2015

RNA-seq analysis reveals genetic response and tolerance mechanisms to Ozone exposure in soybeanBMC Genomics. 2015 Jun 4, Whaley A1, Sheridan J2, Safari S3, Burton A4, Burkey K5, Schlueter J6.

Author information

  • 1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. awhaley9@uncc.edu.
  • 2Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jbeine@uncc.edu.
  • 3Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. ssafari@uncc.edu.
  • 4United States Department of Agriculture, Agricultural Research Service, 3127 Ligon St, Raleigh, NC, 27695, USA. amyburton425@gmail.com.
  • 5United States Department of Agriculture, Agricultural Research Service, 3127 Ligon St, Raleigh, NC, 27695, USA. kent.burkey@ars.usda.gov.
  • 6Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jschluet@uncc.edu.

Abstract

BACKGROUND:

Oxidative stress caused by ground level ozone is a contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is considered to be ozone sensitive, and current research into its response to oxidative stress is limited. To better understand the geneticresponse in soybean to oxidative stress, an RNA-seq analysis of two soybean cultivars was performed comparing an ozone intolerant cultivar (Mandarin-Ottawa) and an ozone resistant cultivar (Fiskeby III) following exposure to ozone.

RESULTS:

Analysis of the transcriptome data revealed cultivar-specific expression level differences of genes previously implicated in oxidative stress responses, indicating unique cultivar-specific responses. Both Fiskeby III and Mandarin (Ottawa) exhibit an increased expression of oxidativeresponse genes as well as glutathiones, phenylpropanoids, and phenylalanine ammonia-lyases. Mandarin (Ottawa) exhibited more general stressresponse genes whereas Fiskeby III had heightened expression of metabolic process genes. An examination of the timing of gene responses over the course of ozone exposure identified significantly more differentially expressed genes across all time points in Mandarin (Ottawa) than in Fiskeby III. The timing of expression was also considered to identify genes that may be indicative of a delayed response to ozone stress in Fiskeby III, We found that Mandarin (Ottawa) exhibits an higher level of expression in early time points for oxidative and general stress response genes while Fiskeby III seems to maintain expression of defense and stress response genes. Of particular interest was the expression of wax and cutin biosynthetic genes that we found to be expressed in Mandarin (Ottawa) in all sampled time points, whereas the expression of this pathway is only in the first time point for Fiskeby III.

CONCLUSIONS:

We were able to identify differentially expressed genes that correspond to each of the known or expected categories of genes previously implicated in other species for ozone stress. Our study shows evidence that at least part of the observed ozone tolerance of Fiskeby III may be due to its thicker, denser leaves providing passive resistance thereby limiting the degree of ozone exposure. The observed diminishedgenetic response is then likely a consequence of this reduced exposure.

Comments are closed.

Connect With Us