Identifcation of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis

To understand the gene expression networks controlling soybean seed set and size, transcriptome analyses were performed in three early seed developmental stages, using two genotypes with contrasting seed size. The two-dimensional data set provides a comprehensive and systems-level view on dynamic gene expression networks underpinning soybean seed set and subsequent development. Using pairwise comparisons and weighted gene coexpression network analyses, we identifed modules of coexpressed genes and hub genes for each module. Of particular importance are the discoveries of specifc modules for the large seed size variety and for seed developmental stages. A large number of candidate regulators for seed size, including those involved in hormonal signaling pathways and transcription factors, were transiently and specifcally induced in the early developmental stages. The soybean homologs of a brassinosteroid signaling receptor kinase, a brassinosteroid-signaling kinase, were identifed as hub genes operating in the seed coat network in the early seed maturation stage. Overexpression of a candidate seed size regulatory gene, GmCYP78A5, in transgenic soybean resulted in increased seed size and seed weight. Together, these analyses identifed a large number of potential key regulators controlling soybean seed set, seed size, and, consequently, yield potential, thereby providing new insights into the molecular networks underlying soybean seed development.