title: Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions.
abstract: BACKGROUND
  Soybean is a major crop that provides an important source of protein and oil to humans and animals, but its production can be dramatically decreased by the occurrence of drought stress. Soybeans can survive drought stress if there is a robust and deep root system at the early vegetative growth stage. However, little is known about the genome-wide molecular mechanisms contributing to soybean root system architecture. This study was performed to gain knowledge on transcriptome changes and related molecular mechanisms contributing to soybean root development under water limited conditions.
  
  
  RESULTS
  The soybean Williams 82 genotype was subjected to very mild stress (VMS), mild stress (MS) and severe stress (SS) conditions, as well as recovery from the severe stress after re-watering (SR). In total, 6,609 genes in the roots showed differential expression patterns in response to different water-deficit stress levels. Genes involved in hormone (Auxin/Ethylene), carbohydrate, and cell wall-related metabolism (XTH/lipid/flavonoids/lignin) pathways were differentially regulated in the soybean root system. Several transcription factors (TFs) regulating root growth and responses under varying water-deficit conditions were identified and the expression patterns of six TFs were found to be common across the stress levels. Further analysis on the whole plant level led to the finding of tissue-specific or water-deficit levels specific regulation of transcription factors. Analysis of the over-represented motif of different gene groups revealed several new cis-elements associated with different levels of water deficit. The expression patterns of 18 genes were confirmed byquantitative reverse transcription polymerase chain reaction method and demonstrated the accuracy and effectiveness of RNA-Seq.
  
  
  CONCLUSIONS
  The primary root specific transcriptome in soybean can enable a better understanding of the root response to water deficit conditions. The genes detected in root tissues that were associated with key hormones, carbohydrates, and cell wall-related metabolism could play a vital role in achieving drought tolerance and could be promising candidates for future functional characterization. TFs involved in the soybean root and at the whole plant level could be used for future network analysis between TFs and cis-elements. All of these findings will be helpful in elucidating the molecular mechanisms associated with water stress responses in soybean roots.
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. songli@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. princesj@missouri.edu.
authors.forename: Silvas
authors.initials: S
authors.lastname: Prince
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. valliyodanb@missouri.edu.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. joshitr@missouri.edu.|MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. joshitr@missouri.edu.|Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA. joshitr@missouri.edu.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. maldonadodossantosj@missouri.edu.
authors.forename: Joao V
authors.initials: JV
authors.lastname: Maldonado dos Santos
authors.affiliation: Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. jwqrd@mail.missouri.edu.
authors.forename: Jiaojiao
authors.initials: J
authors.lastname: Wang
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. Linl@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. wanj@missouri.edu.
authors.forename: Jinrong
authors.initials: J
authors.lastname: Wan
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. yongqin.w@gmail.com.
authors.forename: Yongqin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. xudong@missouri.edu.|MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. xudong@missouri.edu.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.edu.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D003681:Dehydration / Q000235:genetics*; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development; D013025:Glycine max / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D014867:Water / Q000378:metabolism
chemical_list: D014867:Water