- 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.
- Research Geneticist, GS11-13, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland (1978-1897)
- Associate Professor of Crop Molecular Biology, Department of Agronomy, University of Illinois (1987-1995)
- Professor of Crop Molecular Biology, Crop Sciences, University of Illinois (1995-2014)
- Adlai Ewing Chair in Soybean Molecular Biology, Crop Sciences, University of Illinois (2004-2014)
- Soybean Functional Genomics and Nanotechnology
In the early applications of genomics for soybean, our lab 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 transcripts in soybean for or 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). 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; George 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. 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 millions of 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 (Zabala et al., 2012). 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. Numerous targets of the small RNAs have been identified by degradome sequencing (Shamimuzzaman and Vodkin, 2012). 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) (Hamamouch et al., 2012). We analyze constructs for the production of the small RNAs using sequencing.
Using RNA-Seq, we are currently determining networks of gene expression in the developing seed and seed coats (Jones and Vodkin, 2010; 2013), seedling cotyledons (Shamimuzzaman and Vodkin, 2014), and in lines with mutations that affect seed or seedling traits (Hunt et al., 2011; Kour et al, 2014). Chromatin immunoprecipitation (CHiP)-Seq has been used to determine the genes that are regulated by particular transcription factors (Shamimuzzaman and Vodkin, 2013).
We have dissected the genetic and molecular basis of mutations that affect the flavonoid pathway, including transposable element mutations that carry host gene fragments (Zabala and Vodkin, 2005; 2007; 2008). Genomic resequencing and methylation sequencing are now also used as approaches to investigate the molecular basis of mutations in soybean.
- Naturally-Occurring RNAi (RNA Interference in Soybean)
We have shown that naturally occurring soybean siRNAs (short interfering RNAs) control the activity of the enzyme chalcone synthase in a tissue specific manner only during seed coat development (Tuteja et al., 2004; 2009; Cho et al., 2013). 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.
The broad areas of research in my laboratory involve gene isolation, regulation, and transfer in higher plants. A major emphasis is to understand how specific plant traits are controlled by gene action at the molecular level. These investigations exploit unusual mutations and unique genetic resources, and they combine a multidisciplinary approach including functional genomics, high throughput âNext Generationâ Sequencing, genetics, bioinformatics, biochemistry, and molecular biology.
Honors, Recognition, and Outstanding Achievements
- Member of Soybean Regeneration and Transformation Team that received the Illinois Soybean Association Excellence in Soybean Research Award, 1996
- Elected to the Council of American Genetic Association, 1994; Secretary 1997-2000
- Selected as Researcher of the Year by the Illinois Soybean Association, 1993
- List of Excellent Instructors at the Univ. of Illinois including 2004, 2007, 2008, 2009, 2011
- Senior Faculty Award for Excellence in Research, College of ACES, 1999
- Paul Funk Award, Colleges of Agriculture, Consumer, and Environmental Sciences, 2003
- Charles Adlai Ewing Endowed Chair in Soybean Molecular Biology, 2004-2014
Selected Articles in Journals
- Zabala, G.C. and Vodkin, L.O. 2003. Cloning of the pleiotropic T locus in soybean and two recessive alleles that differentially affect structure and expression of the encoded flavonoid 3' hydroxylase. Genetics 163: 295-309.
- Thibaud-Nissen, F., Shealy, R. T., Khanna, A., and Vodkin, L.O. 2003. Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol. 132: 118-136.
- Shoemaker, R.C., Schulter, J.A., Cregan, P., Vodkin, L. O. 2003. The status of soybean genomics and its role in the development of soybean biotechnologies. AgBioForum 6: 4-7.
- Stromvik, M. V., Thibaud-Nissen, F., and Vodkin, L. O. 2004. Mining soybean expressed sequence tag and microarray data. Recent Advances in Phytochemistry 38: 177-195.
- Stacey, G., Vodkin, L. O., Parrott, W., and Shoemaker, R.C., 2004 National Science Foundation-sponsored workshop report. Draft plant for soybean Genomics. Plant Physiol 135: 59-70.
- Shoemaker, R.C., Cregan, P.B., and Vodkin, L.O. 2004. Soybean Genomics. In Soybeans: Improvement, Production and Uses, 3rd edition, ASA monograph No. 16, J. Specht (ed). American Society of Agronomy, Madison, WI, pp. 235-263.
- Tuteja, J., Clough, S. J., Chan, W.-C, and Vodkin, L. O. 2004. Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. 2004. Plant Cell 16: 819-835.
- Vodkin, L. O., Khanna, A., Shealy, R. T., Clough, S. J., Gonzalez, O., Philip, R., Zabala, G. C., Thibaud-Nissen, F., Sidarous, M., Stromvik, M. V., Shoop, E. G., Schmidt, C., Retzel, E. F., Erpelding, J., Shoemaker, R. C., Rodrizeuz-Huete, A., Polacco, J. C., Coryell, V., Keim, P., Gong, G., Liu, L., Pardinas, J. L., Schweitzer, P. 2004. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5: 73.
- Clough, S. J., Tuteja, J., Li, M., Marek, L. F., Shoemaker, R. C., and Vodkin, L. O. 2004. Features of 100 kb gene-rich region include an inverted perfect repeat cluster of CHS genes comprising the I locus. Genome 47:819-831.
- Clough, S. J. and Vodkin, L. O., 2004. Soybean microarrays: a genomics tool for crop improvement. In Genomics for Legume Crops, R. Wilson, C. Brummer, T. Stalker (eds). American Oil Chemists Society Press., pp. 267-283.
- Zou, J., Rodriguez-Zas, S., Aldea, M., Li, M., Zhu, J., Gonzalez, D.O., Vodkin, L.O., DeLucia, E., and Clough, S., J. 2005. Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid down regulation of photosynthesis, Mol Plant Microbe Interact. 18: 1161-1174.
- Zabala, G. and Vodkin, L.O. 2005. The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell 17: 2619-2632.
- Strömvik, M.V., Latour, F. and Archambault, A., and Vodkin, L.O. 2006. Extent of Bean pod mottle virus, Soybean mosaic virus and Cowpea chlorotic mottle virus sequences in soybean EST data evidenced by computational analysis. Canadian J. Plant Pathology 28: 289-301.
- Ainsworth, E.A., Rogers, A., Vodkin, L.O., Walter, A. and Schurr, U. 2006. The effects of elevated CO2 on soybean gene expression: An analysis of growing and mature leaves. Plant Physiol. 142: 135-147.
- Zabala, G., Zou, J., Tuteja, J., Gonzalez, D.O., Clough, S. J., and Vodkin, L.O. Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. 2006. BMC Plant Biology 6: 26.
- Vodkin, L. O., Thibaud-Nissen, F., Gonzalez, D. O., Zabala, G., Clough, S. J., and Shealy, R. 2007. An updatae on soybean functional genomics and microarray resources for gene discovery and crop improvement. Petria 17: 43-53.
- Zabala, G. and Vodkin, L. O. 2007. Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biol 7:38.
- Zabala, G. and Vodkin, L. O. 2007. A rearrangement resulting in small tandem repeats in the F3’5’H gene of white flower genotypes is associated with the soybean W1 locus. Plant Genome 47: 113-124.
- Gonzalez, D. O. and Vodkin, L.O. 2007. Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development. BMC Genomics 8: 468.
- O’Rourke, J., Graham, M., Vodkin, L.O., Gonzalez, D. O., Cianzio, S. R., and Shoemaker, R. C. 2007. Recovering from iron deficiency chlorosis in near-isogenic soybeans: A microarray study. Plant Physiol and Biochem 47: 287-292.
- O’Rourke, J., Carlson, D., Gonzalez, D. O, Vodkin, L. O., Graham, M.,., Cianzio, S. R., Grusak, M., and Shoemaker, R. C. 2007. Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. BMC Genomics 8: 476.
- Vodkin, L. O., Jones, S., Gonzalez, D. O., Thibaud-Nissen, F., Zabala, G. and Tuteja, J. 2008. Genomics of seed development. In Soybean Genomic, G. Stacey (ed). Springer, N. Y. pp. 163-184.
- Brechenmacher, L., Kim, M-Y., Benitez, M., Li, M., Joshi, T., Calla, B., Lee, M. P., Libault, M., Vodkin, L. O., Xu, D. X., Lee, S-H., Clough, S., and Stacey, G. 2008. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol. Plant Microbe Interact. 21: 621-645.
- Li, Y., Zou, J., Li, M., Bilgin, D., Vodkin, L.O., Hartman., G. L., and Clough, S. J. 2008. Soybean defenses against the soybean aphid. New Phytologist 179: 185-195.
- Tuteja, J. and Vodkin, L.O. 2008. Structural features of the endogenous CHS silencing and target loci in the soybean genome. Plant Genome 48: 49-69.
- Zhu, J., Patzoldt, W., Shealy, R., Vodkin, L., Clough, S., Tranel, P. 2008. Transcriptome response to glyphosate in sensitive and resistant soybean. J. Agri Food Chem. 56:6355-6363.
- Saeed, H., Vodkin, L.O., Fauteux, F., and Strömvik, M.V., 2008. Promoters of the soybean seed lectin homologues Le2 and Le3 regulate expression in vegetative tissues of Arabidopsis. Plant Science 175:868-876.
- Zabala, G. and Vodkin, L. 2008. A putative autonomous 20.5 kb-CACTA transposon insertion in an F3’H allele identifies a new CACTA transposon subfamily in Glycine max. BMC Plant Biology 8:124.
- Gasic, K., Gonzalez, D. O., Thimmapuram, J., et al. Gasic, K.; Gonzalez, D.O., Thimmapuram, J. Malnoy, M., Gong, G., Han, Y., Vodkin, L., Liu, L., Aldwinckle, H., Carroll, N., Orvis, K., Goldsbrough, P., Clifton, S., Pape, D., Fulton, L., Martin, J., Theising, B., Korban, S. 2009. Comparative and functional annotation of a large sequenced tag collection of apple (Malus x domestica). 2009. Plant Genome 2: 23-38.
- Block, I.D., Mathias, P.C., Ganesh, N., Jones, S., Dorvel, B.R., Chaudhery, V., Vodkin, L.O., Bashir, R., and Cunningham, B.T. 2009. A detection Instrument for enhanced fluorescence and label-free imagining on photonic crystal surfaces. Optics Express, 17:13222-13235.
- Block, I.D, Mathias, P.C., Jones, S.I., Vodkin, L.O. and Cunningham, Brian T. 2009. Optimizing the spatial resolution of photonic crystal label-free imaging. Applied Optics 48:6567-6574.
- Tuteja, J.H., Zabala, G., Varala, K., Hudson, M., and Vodkin, L.O. Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats. 2009. Plant Cell 21:3063-3077. [This article was highlighted in an “In This Issue” feature of The Plant Cell by Eckardt, N. A. (Senior Features Editor) (2009). Tissue-specific siRNAs that silence CHS genes in soybean. The Plant Cell. 21: 2983-2984.]
- Mathias, P., Jones, S.I., Wu, H-Y, Yang, F., Ganesh, N., Gonzalex, D.O., Bollero, G., Vodkin, L.O., and Cunningham, B.T. 2010. Improved sensitivity of DNA microarrays using photonic crystal enhanced fluorescence. Analytical Chem. 82:6854-6861.
- George, S., Block, I.D., Jones, S.I., Mathias, P.C., Chaudhery, V., Vuttipittayamongkol, P., Qu, H.-Y., Vodkin, L.O. and Cunningham, B.T. 2010. Label-free prehybridization DNA microarray imaging using photonic crystals for quantitative spot analysis. Analytical Chem 82:8551-8557.
- Jones, S.I., Gonzalez, D.O., and Vodkin, L.O. 2010. Flux of transcript patterns during soybean seed development. BMC Genomics 11:136.
- Hunt, M., Kaur, N., Stromvik, M., and Vodkin, L.O. 2011. Transcript profiling reveals expression differences in wild-type and glabrous soybean lines. BMC Plant Biology 11:145.
- Vodkin, L., Zabala, G., Campos, E., Tuteja, J., and Jones, S. 2012. Tissue-specific regulation of gene expression by siRNAs in soybean. In: Designing Soybeans for 21st Century Markets. R. Wilson (ed). AOCS Press, Urbana, IL, pp. 105-122. (book chapter)
- Hamamouch, N., Li, C., Hewezi, T., Baum, T.J., Mitchum, M., Hussey, R.S. Vodkin, L.O. and Davis, E.L. 2012. The interaction of the novel 30C02 cyst nematode effector protein with a plant beta-1,3 endoglucanase may suppress host defense to promote parasitism. J. of Experimental Botany 63:3683-3695.
- Shamimuzzaman, M. and Vodkin, L.O. 2012. Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genomics 13: 310.
- Zabala G., Campos, E., Varala, K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M. and Vodkin, L. 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biology 12:177.
- Jones, S.I. and Vodkin, L.O. 2013. Using RNA-Seq to profile soybean seed development from fertilization to maturity. PLoS ONE 8(3):e59270.
- Shamimuzzaman, Md and Vodkin, L.O. 2013. Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq. BMC Genomics, 14:477.
- Cho, Y.B., Jones, S.I., Vodkin, L.O. 2013. The transition from primary siRNAs to amplified secondary siRNAs that regulate chalcone synthase during development of Glycine max seed coats. PLos ONE 8 (10):e76954.
- Shamimuzzam, Md and Vodkin, L.O. 2014. Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional Func Intr Genomics DOI 10.1007/s10142-014-0388-x.
- Kour, A., Boone, A.M., Vodkin, L.O. 2014. RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline-Rich and Other Cell Wall Protein Transcripts. PLos ONE 9 (5) e96342.
- Zabala, G. and Vodkin, L.O. 2014. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLos ONE 9:e111959.
- Jacobs, T.B., Lawler, N.J., LaFayette, P.R., Vodkin, L.O., and Parrott, W.A. 2015. Simple gene-silencing using the trans-acting siRNA pathway. Plant Biotechnol. J. doi: 10.1111 /pbi.12362.
- Jones, S.I., Tan, Y., Shamimuzzaman, Md, George, S., Cunningham, B. and Vodkin, L.O. 2015. Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays. Plant Physiol 167: 639-649.