title: Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance.
abstract: BACKGROUND
  Among 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.
  
  
  RESULTS
  Contrasting 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.
  
  
  CONCLUSIONS
  There 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.
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. kaloseidos@hotmail.com.
authors: Jin Hee
authors: JH
authors: Shin
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. jnvaughn@uga.edu.
authors: Justin N
authors: JN
authors: Vaughn
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. hussein@uga.edu.
authors: Hussein
authors: H
authors: Abdel-Haleem
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. mcch@uga.edu.
authors: Carolina
authors: C
authors: Chavarro
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. bla@uga.edu.
authors: Brian
authors: B
authors: Abernathy
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. kkim@uga.edu.
authors: Kyung Do
authors: KD
authors: Kim
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. sjackson@uga.edu.
authors: Scott A
authors: SA
authors: Jackson
authors: Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA. zli@uga.edu.
authors: Zenglu
authors: Z
authors: Li
mesh_terms: D055864:Droughts; D013025:Glycine max / Q000235:genetics / Q000502:physiology*; D059467:Transcriptome; D014867:Water
chemical_list: D014867:Water
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