title: Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.
abstract: BACKGROUND
  Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient and iron deficient conditions.
  
  
  RESULTS
  Transcriptional profiles of soybean (Glycine max, L. Merr) near isogenic lines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) grown under Fe-sufficient and Fe-limited conditions were analyzed and compared using the Affymetrix GeneChip Soybean Genome Array. There were 835 candidate genes in the Clark (PI548553) genotype and 200 candidate genes in the IsoClark (PI547430) genotype putatively involved in soybean's iron stress response. Of these candidate genes, fifty-eight genes in the Clark genotype were identified with a genetic location within known iron efficiency QTL and 21 in the IsoClark genotype. The arrays also identified 170 single feature polymorphisms (SFPs) specific to either Clark or IsoClark. A sliding window analysis of the microarray data and the 7X genome assembly coupled with an iterative model of the data showed the candidate genes are clustered in the genome. An analysis of 5' untranslated regions in the promoter of candidate genes identified 11 conserved motifs in 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier, confirming the cluster analysis results.
  
  
  CONCLUSIONS
  These analyses have identified the first genes with expression patterns that are affected by iron stress and are located within QTL specific to iron deficiency stress. The genetic location and promoter motif analysis results support the hypothesis that the differentially expressed genes are co-regulated. The combined results of all analyses lead us to postulate iron inefficiency in soybean is a result of a mutation in a transcription factor(s), which controls the expression of genes required in inducing an iron stress response.
authors.affiliation: Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USA. utehawk@iastate.edu
authors.forename: Jamie A
authors.initials: JA
authors.lastname: O'Rourke
authors.forename: Rex T
authors.initials: RT
authors.lastname: Nelson
authors.forename: David
authors.initials: D
authors.lastname: Grant
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Steven
authors.initials: S
authors.lastname: Cannon
authors.forename: Carroll P
authors.initials: CP
authors.lastname: Vance
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Graham
authors.forename: Randy C
authors.initials: RC
authors.lastname: Shoemaker
mesh_terms: D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D007501:Iron / Q000378:metabolism; D000090463:Iron Deficiencies; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000235:genetics*; D011401:Promoter Regions, Genetic; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D007501:Iron
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