title: Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.
abstract: Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2724 and 3498 DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri Columbia, MO, USA.
authors.forename: Qiuming
authors.initials: Q
authors.lastname: Yao
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Gunvant B
authors.initials: GB
authors.lastname: Patil
authors.affiliation: Division of Plant Sciences, University of MissouriColumbia, MO, USA; Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Agarwal
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Rupesh K
authors.initials: RK
authors.lastname: Deshmukh
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.affiliation: Division of Plant Sciences, University of MissouriColumbia, MO, USA; Legume Biotechnology Laboratory, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China.
authors.forename: Biao
authors.initials: B
authors.lastname: Wang
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Yongqin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Silvas J
authors.initials: SJ
authors.lastname: Prince
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri Columbia, MO, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Plant Genetics Research Unit, Donald Danforth Plant Science Center, US Department of Agriculture, Agricultural Research Service, Midwest Area St. Louis, MO, USA.
authors.forename: Yongqiang C
authors.initials: YC
authors.lastname: An
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Division of Plant Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
keywords: RNA-Seq; drought; flooding; gene expression; soybean; stress