ARS | Publication request: Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 22, 2009
Publication Date: August 13, 2009
Citation: O'Rourke, J.A., Nelson, R., Grant, D.M., Schmutz, J., Grimwald, J., Cannon, S.B., Vance, C.P., Graham, M.A., Shoemaker, R.C. 2009. Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response. Biomed Central(BMC)Genomics. 10:376. Available: http://www.biomedcentral.com/1471-2164/10/376.

Interpretive Summary: Although iron is one of the most abundant nutrients in the earth's crust, plants often suffer from iron deficiency chlorosis due to the inability of the plant to take up the iron from the soil. Deficiency of iron in plants can cause iron deficiency in children and child-bearing women in many third-world countries. Little is known about the genetic control of iron deficiency in plants. In this study, the authors identified genes that are likely involved in maintenance of iron balance in plants. They classified the genes by function, and then determined where on each of soybean's 20 chromosome pairs each gene was located. They were surprised to find that the genes were clustered in the genome. A more detailed analysis of the genes identified unique DNA sequences, in common among many genes, that control the expression of the genes. This information is important for understanding how iron balance is regulated in soybean and will be useful to geneticists, physiologists and plant breeders.

Technical Abstract: Transcriptional profiles of soybean (Glycine max, L. Merr) near isogenic lines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) were analyzed and compared using the Affymetrix® GeneChip® Soybean Genome Array. A comparison of plants grown under Fe-sufficient and Fe-limited conditions identified 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. These same microarrays also identified 211 single feature polymorphisms (SFPs) specific to either Clark or IsoClark. Sequences of the candidate genes, SFPs, and sequences of markers known to lie within iron QTLs were aligned against the 7X assembly of the soybean whole genome sequence. Fifty-eight differentially expressed genes were identified with a genetic location within known QTLs in the Clark genotype and 21 in the IsoClark genotype. Additionally, 11 SFPs aligned within the known QTL regions. A sliding window analysis of the microarray data and the 7X genome coupled with an iterative simulation model of the data showed the candidate genes exhibit clustering in the genome. An analysis of promoter regions of candidate genes identified 11 conserved motifs in promoter regions of 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier and confirming the cluster analysis results. The combined results of all analyses lead us to believe iron inefficiency in soybean is a result of a mutation in a transcription factor, which controls the expression of genes required in inducing an iron stress response.