Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity.

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  • Additional Information
    • Author-Supplied Keywords:
      Agriculture
      Biology
      Computational biology
      Crops
      Developmental biology
      Genetics and Genomics
      Genome analysis tools
      Genome expression analysis
      Genomics
      Plant genomics
      Plant growth and development
      Plants
      Research Article
      Seeds
      Transcriptomes
    • NAICS/Industry Codes:
      561730 Landscaping Services
      111422 Floriculture Production
      311224 Soybean and Other Oilseed Processing
      411120 Oilseed and grain merchant wholesalers
      111110 Soybean Farming
    • Abstract:
      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. [ABSTRACT FROM AUTHOR]
    • Abstract:
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    • Author Affiliations:
      1Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
    • ISSN:
      1932-6203
    • Accession Number:
      10.1371/journal.pone.0059270
    • Accession Number:
      87681217
  • Citations
    • ABNT:
      JONES, S. I.; VODKIN, L. O. Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity. PLoS ONE, [s. l.], v. 8, n. 3, p. 1–12, 2013. DOI 10.1371/journal.pone.0059270. Disponível em: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=a9h&AN=87681217&custid=s6224580. Acesso em: 18 jan. 2020.
    • AMA:
      Jones SI, Vodkin LO. Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity. PLoS ONE. 2013;8(3):1-12. doi:10.1371/journal.pone.0059270.
    • APA:
      Jones, S. I., & Vodkin, L. O. (2013). Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity. PLoS ONE, 8(3), 1–12. https://doi.org/10.1371/journal.pone.0059270
    • Chicago/Turabian: Author-Date:
      Jones, Sarah I., and Lila O. Vodkin. 2013. “Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity.” PLoS ONE 8 (3): 1–12. doi:10.1371/journal.pone.0059270.
    • Harvard:
      Jones, S. I. and Vodkin, L. O. (2013) ‘Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity’, PLoS ONE, 8(3), pp. 1–12. doi: 10.1371/journal.pone.0059270.
    • Harvard: Australian:
      Jones, SI & Vodkin, LO 2013, ‘Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity’, PLoS ONE, vol. 8, no. 3, pp. 1–12, viewed 18 January 2020, .
    • MLA:
      Jones, Sarah I., and Lila O. Vodkin. “Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity.” PLoS ONE, vol. 8, no. 3, Mar. 2013, pp. 1–12. EBSCOhost, doi:10.1371/journal.pone.0059270.
    • Chicago/Turabian: Humanities:
      Jones, Sarah I., and Lila O. Vodkin. “Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity.” PLoS ONE 8, no. 3 (March 2013): 1–12. doi:10.1371/journal.pone.0059270.
    • Vancouver/ICMJE:
      Jones SI, Vodkin LO. Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity. PLoS ONE [Internet]. 2013 Mar [cited 2020 Jan 18];8(3):1–12. Available from: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=a9h&AN=87681217&custid=s6224580