title: RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean.
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 genetic response 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 oxidative response genes as well as glutathiones, phenylpropanoids, and phenylalanine ammonia-lyases. Mandarin (Ottawa) exhibited more general stress response 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 diminished genetic response is then likely a consequence of this reduced exposure.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. awhaley9@uncc.edu.
authors.forename: Adam
authors.initials: A
authors.lastname: Whaley
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jbeine@uncc.edu.
authors.forename: Jaime
authors.initials: J
authors.lastname: Sheridan
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. ssafari@uncc.edu.
authors.forename: Sajedeh
authors.initials: S
authors.lastname: Safari
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, 3127 Ligon St, Raleigh, NC, 27695, USA. amyburton425@gmail.com.
authors.forename: Amy
authors.initials: A
authors.lastname: Burton
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, 3127 Ligon St, Raleigh, NC, 27695, USA. kent.burkey@ars.usda.gov.
authors.forename: Kent
authors.initials: K
authors.lastname: Burkey
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jschluet@uncc.edu.
authors.forename: Jessica
authors.initials: J
authors.lastname: Schlueter
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D005838:Genotype; D005978:Glutathione / Q000378:metabolism; D008563:Membrane Lipids / Q000096:biosynthesis; D018384:Oxidative Stress / Q000187:drug effects; D010126:Ozone / Q000633:toxicity*; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics / Q000378:metabolism; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000032:analysis / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D014885:Waxes / Q000378:metabolism
chemical_list: D008563:Membrane Lipids; D010940:Plant Proteins; D014885:Waxes; C000521:cutin; D012313:RNA; D010126:Ozone; D010650:Phenylalanine Ammonia-Lyase; D005978:Glutathione