[Illinois] CABPN Workshop: Applications of Genomics and Nanotechnology to Soybean Improvement
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Center for Agricultural, Biomedical, and Pharmaceutical Nanotechnology
From the Dept. of Crop Sciences' Directory:
Soybean Functional Genomics and Nanotechnology
Other projects have developed public genomic resources for soybean including a soybean EST (expressed sequence tag) database (Shoemaker, et al, 2004); cDNA microarrays (Vodkin et al., 2004) and long oligo arrays (Gonzalez et al., 2007). These have been used extensively to profile soybean transcripts during for a diversity of biological questions including reprogramming of transcriptome patterns during somatic embryogenesis (Thibaud-Nissen et al., 2003), early response to challenge by pathogens (Zou et al., 2005), effect of elevated CO2 (Ainsworth et al., 2005), and transcript profiles of seed development (Jones et al, 2010) and germination (Gonzalez and Vodkin, 2007). We are currently determining networks of gene expression in the developing seed and have dissected the genetic and molecular basis of other mutations that affect the flavonoid pathway, including transposable element mutations that carry host gene fragments (Zabala and Vodkin, 2005; 2007; 2008). These projects also led to extensive collaborations with nanotechnologists on campus to improve the sensitivity of detecting gene changes using microarrays (Mathias et al., 2010).
Transcriptomics and Function of Small RNAs in Soybean
Recent projects utilize high throughput transcriptomics (mRNAseq) and small RNA sequencing to determine the genes expressed during seed development and in various mutant lines. We explore the mRNA and small RNA populations for many stages and tissues of soybean seed and seedling development by using Illumina Sequence-by-Synthesis deep sequencing that yields over 50 million reads for each sample. The quantitative levels of mRNAs are determined and mapped to the soybean genome. Many small RNAs match known miRNAs (microRNAs) from other organisms, while many others appear to be novel siRNAs or miRNAs. Similar to the coding transcriptome, the small RNAome reveals many organ, tissue specific and developmental shifts in the population of small RNAs. We correlate the changes in small RNA populations to those of the mRNAs as elucidated by mRNAseq during seed development. In addition, we compare selected mutant isolines that affect nutritional content, morphological, and/or disease resistance traits to determine how these traits are controlled. Finally, we are part of a multi-university consortium to improve soybean transformation (Widholm et al., 2009) and to engineer resistance to the soybean cyst nematode by genetic engineering using RNAi (RNA interference). We analyze constructs for production of the small RNAs using sequencing.
Naturally-Occurring RNAi (RNA Interference in Soybean)
We have shown that naturally occurring soybean siRNAs (short interfering small RNAs) control the activity of the enzyme chalcone synthase in a tissue specific manner only during seed coat development (Tuteja and Vodkin, 2008; Tuteja et al., 2004; 2009). All commercially used soybeans contain this mechanism that shuts off the pigment pathway only in seed coats and not in the seed proper (cotyledons) where the isoflavones and other polyphenol antioxidant compounds are produced in the soybean seed.
From the Dept. of Crop Sciences' Directory:
Ph.D.: Genetics, North Carolina State University, Raleigh, N.C. M.S.: Biology, University of South Carolina, Columbia, S.C. B.S.: Physics, University of South Carolina, Columbia, S.C.
Honors and Awards Charles Adlai Ewing Endowed Chair in Soybean Molecular Biology, 2004-present Paul Funk Award, Colleges of Agriculture, Consumer, and Environmental Sciences, 2003 Senior Faculty Award for Excellence in Research, College of ACES, 1999 List of Excellent Instructors at the Univ. of Illinois including 2004, 2007-9 Selected as Researcher of the Year by the Illinois Soybean Association, 1993 Elected to the Council of American Genetic Association, 1994; Secretary 1997-2000 Member of Soybean Regeneration and Transformation Team that received the Illinois Soybean Association Excellence in Soybean Research Award, 1996
Researchers should cite this work as follows:
Lila Vodkin (2013), "[Illinois] CABPN Workshop: Applications of Genomics and Nanotechnology to Soybean Improvement," https://nanohub.org/resources/16658.
University of Illinois, Urbana-Champaign, IL