Poster: Genomics Resources

Abs # 958: Global expression in soybean using microarrays with a low redundancy 27,000 cDNA "unigene" set

Presenter:	Vodkin, Lila , l-vodkin@uiuc.edu
Authors	Vodkin, Lila  (A)   Clough, Steve  (A)   Shealy, Robin  (A)   Khanna, Anupama  (A)   Thibaud-Nissen, Francoise  (A)   Gonzalez, Orlando  (A)   Zabala, Gracia  (A)   Philip, Reena  (A)   Shoop, Elizabeth  (B)   Schmidt, Christina  (B)   Stromvik, Martina  (B)   Retzel, Ernest  (B)   Polacco, Joseph  (C)   Keim, Paul  (D)   Shoemaker, Randy  (E)
Affiliations:	(A): University of Illinois (B): University of Minnesota (C): University of Missouri (D): Northern Arizona University (E): Iowa State University

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". The current "unigene" collection (or tentatively unique sequences) represents low redundancy sets of 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); and Gm-c1088 (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. The inserts were amplified from each clone by PCR and were spotted onto glass slides for microarray analysis. Three arrays have been produced, each with approximately 9,216 cDNAs. The arrays have been used to examine gene expression during the reprogramming of cotyledon cells associated with induction of somatic embryos in soybean tissue culture and in transgenic plants (Thibaud-Nissen, et al., Plant Physiol, in press) and to examine isogenic lines containing mutations in the flavonoid pathway. Web sites for the project: http://soybeangenomics.cropsci.uiuc.edu/ and http://web.ahc.umn.edu/biodata