ABSTRACT: Background: To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. Results: It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of largest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages. Conclusions: Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination. Five stages of development of soybean cotyledons were studied. The first three, with fresh weights of 25-50mg, 75-100mg, and 400-500mg, were green in color. The last two, yellow-colored cotyledons with a fresh weight of 200-300mg and dry whole seeds approximately 100-200mg in weight, were desiccating and yellow/brown in color. The green stage of 100-200mg fresh weight cotyledons was used as a reference for all other stages. Four replicates, including two dye swaps, were made of each of the first three (green) stages. Two replicates, including one dye swap, were made of each of the last two (yellow/dry) stages. The results from three different platforms (GPL229, GPL1012, and GPL1013) were combined.
