title: Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress.
abstract: BACKGROUND
  The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement.
  
  
  RESULTS
  In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~13 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses.
  
  
  CONCLUSIONS
  We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
authors.forename: Vikas
authors.initials: V
authors.lastname: Belamkar
authors.forename: Nathan T
authors.initials: NT
authors.lastname: Weeks
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Graham
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA. steven.cannon@ars.usda.gov.
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D003681:Dehydration / Q000235:genetics*; D018628:Gene Dosage; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018398:Homeodomain Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D016350:Leucine Zippers / Q000235:genetics*; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D059372:Nucleotide Motifs; D009928:Organ Specificity / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D054730:Protein Interaction Domains and Motifs; D055049:Salt Tolerance / Q000235:genetics*; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism*; D013312:Stress, Physiological; D014157:Transcription Factors / Q000737:chemistry / Q000145:classification / Q000235:genetics*
chemical_list: D018398:Homeodomain Proteins; D014157:Transcription Factors