Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 6/30/2004
Publication Date: 8/8/2004
Citation: Gonzales, D., Thibaud-Nissen, F., Clough, S.J., Stromvik, M., Retzel, E., Vodkin, L. 2004. Global expression analyses using microarrays of a soybean cdna unigene set. Plant and Animal Genome Conference Proceedings. p. 115.
Technical Abstract: As part of the NSF-sponsored Soybean Functional Genomics Program, we have accumulated a set of unique genes from a larger collection of soybean 5'ESTs. The current unigene collection (or tentatively unique sequences)represents 36,000 low redundancy cDNA clones. These include reracked libraries Gm-r1070 (a set of 9216 cDNA clones from various stages of immature cotyledons, flowers, pods, and seed coats); Gm-r1021 plus Gm-r1083(a set of approximately 9216 cDNA clones from 8-day old seedling roots,seedling roots inoculated with B. japonicum, whole seedlings, and 2 month old roots); Gm-r1088 and Gm-r1089 (a collection of 9216 cDNA clones from a number of libraries made from cotyledons and hypocotyls of germinating seedlings and leaves and other plant parts subjected to various pathogens or environmental stress conditions). Functional assignments of clones were inferred by matching the BLASTX hits of the 5' and 3' sequences to the non-redundant databases. The inserts were amplified from each clone by PCR and were spotted onto glass slides for microarray analysis. Four arrays have been produced, each with approximately 9,216 cDNAs. We are currently using these arrays to study gene expression during soybean seed development (see poster by Jones, et. al.); during reprogramming of cotyledon cells associated with induction of somatic embryos in soybean tissue culture (Thibaud-Nissen, et al., Plant Physiol, 132:118-136, 2003),and to analyze isogenic lines containing mutations in the flavonoid pathway.