Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.

Reference Report for RTN20151125.14

Title:	Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.
Authors:	O'Rourke, J.A., Nelson, R.T., Grant, D., Schmutz, J., Grimwood, J., Cannon, S., Vance, C.P., Graham, M.A., Shoemaker, R.C.
Source:	BMC Genomics 2009, 10:376
Abstract:	BACKGROUND: Soybeans grown in the upper Midwestern United States often sufferfrom iron deficiency chlorosis, which results in yield loss at the end of theseason. To better understand the effect of iron availability on soybean yield, weidentified genes in two near isogenic lines with changes in expression patternswhen plants were grown in iron sufficient and iron deficient conditions.RESULTS: Transcriptional profiles of soybean (Glycine max, L. Merr) near isogeniclines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) grown under Fe-sufficient and Fe-limited conditions were analyzed and comparedusing the Affymetrix GeneChip Soybean Genome Array. There were 835 candidategenes in the Clark (PI548553) genotype and 200 candidate genes in the IsoClark(PI547430) genotype putatively involved in soybean's iron stress response. Ofthese candidate genes, fifty-eight genes in the Clark genotype were identifiedwith a genetic location within known iron efficiency QTL and 21 in the IsoClarkgenotype. The arrays also identified 170 single feature polymorphisms (SFPs)specific to either Clark or IsoClark. A sliding window analysis of the microarraydata and the 7X genome assembly coupled with an iterative model of the datashowed the candidate genes are clustered in the genome. An analysis of 5'untranslated regions in the promoter of candidate genes identified 11 conservedmotifs in 248 differentially expressed genes, all from the Clark genotype,representing 129 clusters identified earlier, confirming the cluster analysisresults. CONCLUSION: These analyses have identified the first genes with expressionpatterns 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 insoybean is a result of a mutation in a transcription factor(s), which controlsthe expression of genes required in inducing an iron stress response.

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA

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