Systems characterization of gene regulatory networks underlying soybean seed maturation

Seed maturation and its accompanying seed reserve production are accomplished through the concerted activity of many gene products and biological pathways.   To delineate the underlying transcriptional gene regulatory networks that control seed reserve production we examined the transcriptomes of soybean cotyledons at six distinct seed maturation stages We used the cotyledon transcriptome data, in addition to 115 transcriptomes of various soybean seed related tissues, to infer 305 transcription factor regulatory networks. In addition, we sequenced 292 million small RNAs from 18 small RNA libraries from identical cotyledon tissues, and identified 129 novel cotyledon microRNAs. Fifty-four miRNAs were significantly differentially regulated, as measured by accumulation levels, over the course of seed maturation. A rich presence of intronic miRNAs and a high miRNA gain/loss rate were observed in cotyledons. Expression patterns of the cotyledon miRNAs and their predicted target transcripts were compared so as to predict their functional miRNA-target mRNA interactions based on a negative correlation of their expression patterns.  The topology of the cotyledon miRNAs in the transcription factor gene networks was determined and biological pathways that are potentially regulated by the transcription factor networks were identified. The knowledge of the gene regulatory networks and identification of the key regulatory genes enable the design of effective strategies for improving soybean seed quality and production. The research is supported by USDA/ARS and the United Soybean Board.