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

BMC Plant Biology

Research Article

Jin Hee Shin¹  Scott A Jackson¹  Carolina Chavarro¹  Justin N Vaughn¹  Brian Abernathy¹  Hussein Abdel-Haleem¹  Kyung Do Kim¹  Zenglu Li¹ 

[1] Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, 30602, Athens, GA, USA;

关键词: Drought stress;    Canopy-wilting;    Glycine max;    RNA-Sequencing;    Quantitative trait loci (QTL);    Genotype x environment;   

DOI  :  10.1186/s12870-015-0422-8

 received in 2014-08-26, accepted in 2015-01-12,  发布年份 2015

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Shin et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.