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Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance

Overview of attention for article published in BMC Plant Biology, February 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (85th percentile)
  • High Attention Score compared to outputs of the same age and source (90th percentile)

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1 blog
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Title
Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance
Published in
BMC Plant Biology, February 2015
DOI 10.1186/s12870-015-0422-8
Pubmed ID
Authors

Jin Hee Shin, Justin N Vaughn, Hussein Abdel-Haleem, Carolina Chavarro, Brian Abernathy, Kyung Do Kim, Scott A Jackson, Zenglu Li

Abstract

BackgroundAmong abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean.ResultsContrasting data from PI 416937 and the cultivar `Benning¿, we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit, noting both the well-known reduction in photosynthesis genes as well as the less understood up-regulation of the protein transport pathway. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI 416937¿s unique drought avoidance strategy.ConclusionsThere is a general and functionally significant transcriptional response to water deficit that involves not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Genes that show a genotypic difference are more likely to show an environmental response than genes that are constant between genotypes. In this study, at least five genes that clearly exhibited a genotype x environment response fell within known QTL and are very good candidates for further research into slow-wilting.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Chile 1 2%
Brazil 1 2%
Argentina 1 2%
Spain 1 2%
United States 1 2%
Unknown 49 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 26%
Researcher 13 24%
Student > Master 5 9%
Student > Doctoral Student 5 9%
Student > Bachelor 4 7%
Other 7 13%
Unknown 6 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 36 67%
Biochemistry, Genetics and Molecular Biology 4 7%
Engineering 3 6%
Computer Science 2 4%
Environmental Science 1 2%
Other 2 4%
Unknown 6 11%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 18 May 2015.
All research outputs
#3,550,697
of 22,786,087 outputs
Outputs from BMC Plant Biology
#213
of 3,241 outputs
Outputs of similar age
#51,854
of 352,352 outputs
Outputs of similar age from BMC Plant Biology
#8
of 88 outputs
Altmetric has tracked 22,786,087 research outputs across all sources so far. Compared to these this one has done well and is in the 84th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,241 research outputs from this source. They receive a mean Attention Score of 3.0. This one has done particularly well, scoring higher than 93% of its peers.
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 352,352 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 85% of its contemporaries.
We're also able to compare this research output to 88 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 90% of its contemporaries.