Identification of differentially expressed genes between developing seeds of different soybean cultivars

Rongshuang Lin, Jane Glazebrook, Fumiaki Katagiri, James H Orf, Sue Gibson

Research output: Contribution to journalArticlepeer-review


Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits. Others of these probe sets may be involved in regulation of general seed development or metabolism. All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (, under accession number GSE21598.

Original languageEnglish (US)
Pages (from-to)92-98
Number of pages7
JournalGenomics Data
StatePublished - Dec 1 2015

Bibliographical note

Funding Information:
We thank the University of Minnesota Discovery Grant program, the Minnesota Soybean Research & Promotion Council ( 5-08N , 15-09C , 667307-17-10C and 8-11C ), the University of Minnesota Initiative for Renewable Energy and the Environment ( RM-0001-09 ) and the Consortium for Plant Biotechnology Research ( GO12026-304/DE-FG36-02GO12026-008 ) for financial support of this project. None of these sponsors played any role in the design of the experiments, the collection, analysis or interpretation of the data, or the writing or submission of this manuscript. We thank Mr. Phil Schaus for aiding in planting and caring for the soybean lines used in these experiments. We also thank the BioMedical Genomics Center-MicroArray Facility, University of Minnesota for conducting the Affymetrix GeneChip hybridization experiments and the University of Minnesota Supercomputing Institute for assisting in data analysis. We thank Drs. Steve Wanamaker and Timothy J. Close for helping with HarVEST:SoyChip software and Dr. Michelle Graham for providing the Affymetrix Soychip annotations.


  • Composition
  • Seed
  • Soybean
  • Transcriptional profiling
  • Yield

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