Using RNA-Seq to profile soybean seed development from fertilization to maturity

PLoS One. 2013;8(3):e59270. doi: 10.1371/journal.pone.0059270. Epub 2013 Mar 15.


To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes encoding storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. More significantly, the power of RNA-Seq to detect genes expressed at low levels revealed hundreds of transcription factors with notable expression in at least one stage of seed development. Results from a second biological replicate demonstrate high reproducibility of these data revealing a comprehensive view of the transciptome of seed development in the cultivar Williams, the reference cultivar for the first soybean genome sequence.

MeSH terms

  • Antigens, Plant / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Gene Expression Regulation, Plant*
  • Globulins / genetics
  • High-Throughput Nucleotide Sequencing
  • Models, Genetic
  • Plant Proteins / genetics
  • Pollination
  • Seed Storage Proteins / genetics
  • Seeds / genetics*
  • Seeds / growth & development
  • Sequence Analysis, RNA*
  • Soybean Proteins / genetics
  • Soybeans / genetics*
  • Soybeans / growth & development
  • Transcriptome*


  • Antigens, Plant
  • Globulins
  • Plant Proteins
  • Seed Storage Proteins
  • Soybean Proteins
  • beta-conglycinin protein, Glycine max
  • late embryogenesis abundant protein, plant
  • dehydrin proteins, plant
  • glycinin

Grant support

This research was supported by grants from the Illinois Soybean Association, the United Soybean Board, and the Illinois-Missouri Biotechnology Alliance. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.