Predicting transcriptional circuitry underlying seed coat development

• The seed coat is a complex multicellular structure of the seed.
• Large-scale datasets are used to predict transcriptional circuits underlying seed coat development in model oilseeds.
• Methods to build transcriptional modules are discussed.
• We highlight the challenges of mining large-scale datasets and the need to validate transcriptional modules.

Filling, protection, and dispersal of angiosperm seeds are largely dependent on the development of the maternally derived seed coat. The development of the seed coat in plants such as Arabidopsis thaliana and Glycine max (soybean) is regulated by a complex network of genes and gene products responsible for the establishment and identity of this multicellular structure. Recent studies support the hypothesis that the structure, development, and function of the seed coat are under the control of transcriptional regulators that are specified in space and time. Furthermore, these transcriptional regulators can act in combination to orchestrate the expression of large gene sets. We discuss the underlying transcriptional circuits of the seed coat sub-regions through the interrogation of large-scale datasets, and also provide some ideas on how the identification and analysis of these datasets can be further improved in these two model oilseed systems.