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

Overview of attention for article published in BMC Genomics, June 2015
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Title
RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean
Published in
BMC Genomics, June 2015
DOI 10.1186/s12864-015-1637-7
Pubmed ID
Authors

Adam Whaley, Jaime Sheridan, Sajedeh Safari, Amy Burton, Kent Burkey, Jessica Schlueter

Abstract

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. 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. 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 56 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Benin 1 2%
Slovakia 1 2%
Unknown 54 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 18%
Researcher 8 14%
Student > Master 7 13%
Student > Doctoral Student 5 9%
Student > Bachelor 4 7%
Other 7 13%
Unknown 15 27%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 39%
Biochemistry, Genetics and Molecular Biology 5 9%
Computer Science 3 5%
Veterinary Science and Veterinary Medicine 2 4%
Environmental Science 2 4%
Other 5 9%
Unknown 17 30%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 June 2015.
All research outputs
#13,945,480
of 22,808,725 outputs
Outputs from BMC Genomics
#5,345
of 10,651 outputs
Outputs of similar age
#133,672
of 267,109 outputs
Outputs of similar age from BMC Genomics
#127
of 238 outputs
Altmetric has tracked 22,808,725 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,651 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 46th percentile – i.e., 46% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 267,109 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 238 others from the same source and published within six weeks on either side of this one. This one is in the 39th percentile – i.e., 39% of its contemporaries scored the same or lower than it.