title: Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis.
abstract: 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 identified modules of coexpressed genes and hub genes for each module. Of particular importance are the discoveries of specific 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 specifically induced in the early developmental stages. The soybean homologs of a brassinosteroid signaling receptor kinase, a brassinosteroid-signaling kinase, were identified 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 identified 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.
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Du
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors.forename: Shoudong
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors.forename: Cunman
authors.initials: C
authors.lastname: He
authors.affiliation: Institute of Crop Science, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhou
authors.affiliation: School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
authors.forename: Yong-Ling
authors.initials: YL
authors.lastname: Ruan
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors.forename: Huixia
authors.initials: H
authors.lastname: Shou
mesh_terms: D049109:Cell Proliferation / Q000235:genetics* / Q000502:physiology*; D018556:Crops, Agricultural / Q000235:genetics / Q000502:physiology; D007887:Fabaceae / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D012639:Seeds / Q000235:genetics* / Q000502:physiology*; D013025:Glycine max / Q000235:genetics* / Q000502:physiology*
keywords: Seed development; seed number; seed size; soybean; transcriptomic analysis.