Submitted to: Plant and Animal Genome
Publication Type: Proceedings
Publication Acceptance Date: 10/1/2004
Publication Date: 1/4/2005
Citation: Vodkin, L., Shealy, R., Khanna, A., Thibaud-Nissen, F., Clough, S.J., Philip, R., Shoop, E., Schmidt, C., Retzel, E. 2005. Gene functional analysis in soybean by microarray. Plant and Animal Genome. p. 54.
Technical Abstract: DNA microarrays are powerful tools to analyze the expression patterns of thousands of genes simultaneously. As part of the NSF-sponsored Soybean Functional Genomics Program, we are accumulating a set of unique genes from a larger collection of soybean 5' ESTs developed by the Public EST Project for Soybean (in collaboration with the laboratories of Randy Shoemaker and Paul Keim). To date, we have prepared a unigene set of 13,305 genes from cDNA libraries made to mRNA extracted from developing cotyledons and seed coats, young pods, immature and mature flowers, and 7-day seedling roots. After cluster analysis, we selected each singleton and the 5' most read of each contig for additional sequencing at the 3' end. Functional assignments for these 13,305 clones were inferred by matching the blastx matches of the 5' and 3' sequences to the best MetaFam superset of proteins. The inserts were amplified from each clone by PCR and were spotted onto glass slides for microarray analysis. One array contained 9,216 genes spotted once and another one contained 4089 clones spotted twice. Several projects with microarrays will be summarized including their use to profile tissue-specific gene expression and developmental changes in gene expression. In another project, we have examined gene expression during the reprogramming of cotyledon cells associated with induction of somatic embryos in soybean tissue culture (see abstract by Thibaud-Nissen). The final goal of this portion of the NSF project is to generate a unigene set composed of 30,000 genes. Web sites: http://web.ahc.umn.edu/biodata, http://soybeangenomics.cropsci.uiuc.edu/, http://18.104.22.168/soybeanest.html.