ARS | Publication request: The Circadian Clock-Controlled Transcriptome of Developing Soybean Seeds.

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 21, 2009
Publication Date: July 1, 2010
Citation: Hudson, K.A. 2010. The Circadian Clock-Controlled Transcriptome of Developing Soybean Seeds. The Plant Genome. 3(1):1-11.

Interpretive Summary: While many plant genes are controlled by daily changes in the environment such as sunrise or temperature changes, the expression of a large number of genes in model plants is known to be influenced by an endogenous circadian clock that can drive rhythmic expression of genes even in the absence of these external cues. The genes that the clock controls are involved in many different processes such as protein synthesis, photosynthesis, and oil biosynthesis. In order to improve soybean seed composition and yield, it is important to identify which genes in the seed are controlled by the clock, and identify the pathways that they are involved in. In this work over 480 genes were identified that are expressed rhythmically, at the same time each day in the developing soybean seeds. DNA sequences in the promoters of these genes were identified that may be involved in specifying their expression to certain times of day. Unexpectedly, it was also observed that a number of these genes are expressed at different times in the leaves and seeds of the same soybean plants, which indicates it is likely that communication from the mother plant synchronizes gene expression in developing seeds every day. This finding sheds new light on how gene expression is controlled in the seed, and this information will be useful in future efforts by researchers to modify the protein and oil levels in seeds for improved nutrition, and to increase soybean seed yield.

Technical Abstract: A number of metabolic and physiological processes in plants are controlled by the circadian clock, which enables the plant to anticipate daily changes in the environment. Microarray expression profiling was used to identify circadian clock controlled genes expressed in developing soybean seeds. 1.8% of the seed transcriptome was expressed in a circadian rhythm, including genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis. Known circadian and light-controlled promoter elements were identified in the promoters of clock controlled genes. It was found that a number of genes with roles in photosynthesis and carbon metabolism were expressed in different phases in leaves and developing seeds from the same plants under free-running conditions but were expressed synchronously in diurnal conditions. These results provide insight into organ specific phasing of clock controlled gene expression.