Submitted to: Petria
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/17/2007
Publication Date: 6/30/2007
Citation: Vodkin, L.O., Thibaud-Nissen, F., Gonzales, D.O., Zabala, G., Clough, S.J., Shealy, R. 2007. An Update on Soybean Functional Genomics and Microarray Resources for Gene Discovery and Crop Improvement. Petria. 17(1):43-53.
Interpretive Summary: Measuring the expression of each of many thousand genes is important to understanding how an organism functions. In this research the authors took advantage of a public soybean resource to create experimental tools that allow them to measure levels of gene expression, nearly 38,000 genes at a time. They went on to demonstrate that sensitivity of the tool was great enough to distinguish expression levels in a single gene. Robots are capable of printing droplets of solution containing specific genes on a glass microscope slide. As these spots are approximately 1/10th of a millimeter, one can print 10-20,000 different genes on a single standard microscope slide. Constructing microarrays are expensive and time-consuming, however once they are produced their uses are endless for they can be used to obtain a gene expression report from virtually any tissue, at any time, after any treatment. Microarray use is limited only by investigator’s curiosity. The greater the number of diverse microarray experiments that are performed, that greater will be the research community’s ability to determine more completely what is it that a given gene or stimulus does as well as when and why the gene is expressed. The data will also identify new genes that are critical for specific functions. Use of microarrays to analyze mutants will be highly valuable as it will allow scientists to decipher pathways and identify how one gene may block a particular behavior or response. The ability to measure the expression of genes will be critical to scientists researching the complexity of multi-gene inheritance and to predict the possible function of genes for which we have no detailed information. This research will have significant benefits to soybean geneticists, breeders, and the soy industries including, ultimately, the consumer.
Technical Abstract: DNA microarrays are powerful tools to analyze the expression patterns of thousands of genes simultaneously. We review recent soybean genomics projects that have produced public-sector resources for this important legume crop. 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 developed by the “Public EST Project for Soybean” that was sponsored by the soybean grower associations. The current soybean “unigene’ collection (or tentatively unique sequences) represents a set of 36,000 low redundancy cDNA clones derived from over 300,000 expressed sequence tags of cDNAs constructed from 80 libraries that represent a number of tissue and organ systems of the soybean plant grown under various physiological and stress conditions. The cDNA inserts were amplified from each clone by PCR and were spotted onto glass slides for microarray analysis initially with 9,216 cDNAs per array. We currently print 18,432 of the unigene cDNAs per each of two separate arrays, known as the 18k-A and 18k-B soybean microarrays. We review the use of the soybean microarray slides to examine global gene expression patterns during the reprogramming of cotyledon cells associated with induction of somatic embryos in soybean tissue culture. Many other uses of the arrays are currently in progress.