Molecular Genetics and Soybean Genomics Laboratory

Henry T. Nguyen, Ph.D.
Curators' Distinguished
Professor of Plant Sciences,
Division of Plant Sciences
University of Missouri
Tel: 573-882-5494
Fax: 573-882-1469
Henry Nguyen

Babu Valliyodan

Senior Research Scientist

Division of Plant Sciences
41 Agriculture Building
University of Missouri
Columbia, MO 65211

Office: (573) 884-6313
Fax: (573) 882-1469

Lab Member Since: 2003

Current Research Focus:

Develop and establish integrated functional genomics leading to systems biology approach to dissect abiotic stress tolerance mechanisms and yield improvement traits in plants. Large scale sequencing of the most diverse soybean germplasm in the U.S. along with the generation of additional reference genomes and pan genomes for both cultivated and wild-type soybeans using new generation sequencing technologies. Discovery of genomic regions affecting yield using whole genome sequencing technologies leading to the development of functional markers for genomics-assisted breeding strategies for better plant performance and enhanced yield.  Genome sequence information and HapMap from these studies will help the U.S. soybean community to conduct genome wide analyses and identify alleles associated with agronomically important traits.



Ph.D. Plant Biology (Biochemistry and Molecular Biology)
M.S. Plant Biology
B.S. Major Biology, Minor Chemistry

Selected Book Chapters:
  • Valliyodan B, Nguyen HT. Biological Mechanisms that Influence Soy Protein Concentration and Composition. In: Wilson R, ed, Designing Soybeans for the 21st Century Markets. AOCS, IL, USA, 2012.
  • Valliyodan B, Lee J-D, Shannon GJ, Nguyne HT (2011) Soybean. In: Kole C and Joshi CP, eds, Handbook of Bioenergy Crop Plants. CRC Press. USA.
  • Valliyodan B, Nguyen HT (2008) Genomics of Abiotic Stress in Soybean. In: Soybean Genomics, G. Stacey (Ed). Springer Verlag, New York.
  • Vuong TD, Wu X, Pathan Md S, Valliyodan B, Nguyen HT (2007) Genomics approaches to soybean improvement. In: Genomics Assisted Crop Improvement, R.K. Varshney and R. Tuberosa (Eds). Springer Verlag, USA.
  • Sharmistha B, Valliyodan B, Bansal KC (2001) Bio-engineering for reducing post-harvest losses in vegetable crops. In: Emerging scenario in vegetable research and development, G. Kalloo and K. Singh (Eds). Research book Publishing House, New Delhi, India.
Selected Research Publications (*Equal First Author):
  • Valliyodan B, Qui D, Patil G, Zeng P, Huang J, Dai L, Chengxuan C, Zeng L, Joshi T, Vuong T, Musket T, Xu D, Shannon J.G., Shifeng C, Liu X, Nguyen H. T. 2016. Landscape of genomic diversity and trait discovery in soybean. Scientific Reports (Accepted)
  • Chai C, Wang Y, Valliyodan B, Nguyen H. T. 2016. Comprehensive analysis of the soybean (Glycine max) GmLAX auxin transporter gene family. Frontiers in Plant Sci. (Accepted)
  • Maldonado Dos Santos JV, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, Oliveira MF, Marcelino-Guimarães FC, Xu D, Nguyen HT, Abdelnoor RV. 2016. Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. BMC Genomics. 17(1):110.
  • Patil G, Do T, Vuong T.D, Valliyodan B, Lee J-D, Chaudhary J, Shannon G. J, Nguyen H.T (2015) Genomic-assisted haplotype analysis and development of high-throughput SNP markers for salinity tolerance in soybean. Scientific Reports 6:19199.
  • Kadam S, Vuong TD, Qiu D, Meinhardt CG, Song L, Deshmukh R, Patil G, Wan J, Valliyodan B, Scaboo AM, Shannon JG, Nguyen HT. 2016. Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding. Plant Science doi:10.1016/j.plantsci.2015.08.015.
  • Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen H. T, Zhang J, Xu D (2015) A Bayesian Model for Detection of High-order Interactions among Genetic Variants in Genome-wide Association Studies. BMC Genomics 16:1011.
  • Song L, Prince S, Valliyodan B, Joshi T, Maldonado Dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nguyen HT. 2016 Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics 17(1):57.
  • Wang Y*, Chai C*, Valliyodan B, Maupin C, Annen B, Nguyen H. T (2015) Genome-wide analysis and expression profiling of the PIN auxin transporter gene family in soybean (Glycine max). BMC Genomics 16:1011.
  • Chaudhary J, Patil G. B, Sonah H, Deshmukh R. K, Vuong T. D, Valliyodan B, Nguyen H. T. (2015) Expanding omics resources for improvement of soybean seed composition traits. Front. Plant Sci. - Plant Genetics and Genomics 6:1021.
  • Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor Mdos S, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT (2015). Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Sci. 240:65-78.
  • Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M. 2015. Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol. J. (Special Issue on Genomics) doi: 10.1111/pbi.12467.
  • Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. 2015. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci. - Plant Genetics and Genomics 6: 563.
  • Patil G, Valliyodan B, Deshmukh R, Prince S, Nicander B, Zhao M, Sonah H, Song L, Lin L, Chaudhary J, Liu Y, Joshi T, Xu D, Nguyen HT. (2015) Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. BMC Genomics.16:520.
  • Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. (2015) Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance. BMC Genomics 16(1):596.
  • Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W, Valliyodan B, Joshi T, Khan S, Nguyen HT. 2015. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. J Exp Bot. pii: erv407. [Epub ahead of print]
  • Chen W, He S, Liu D, Patil GB, Zhai H, Wang F, Stephenson TJ, Wang Y, Wang B, Valliyodan B, Nguyen HT, Liu Q. A Sweet potato Geranylgeranyl Pyrophosphate Synthase Gene, IbGGPS, Increases Carotenoid Content and Enhances Osmotic Stress Tolerance in Arabidopsis thaliana. PLoS One. 10(9):e0137623.
  • Prince SJ, Murphy M, Mutava RN, Zhang Z, Nguyen N, Ha Kim Y, Pathan SM, Shannon GJ, Valliyodan B, Nguyen HT. (2015) Evaluation of high yielding soybean germplasm under water limitation. J Integr Plant Biol. doi: 10.1111/jipb.12378.
  • Prince SJ, Song L, Qiu D, Maldonado Dos Santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong TD, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MA, Xu D, Shannon JG, Nguyen HT. 2015. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics.16:132.
  • Qiu D, Vuong T, Valliyodan B, Shi H, Guo B, Shannon JG, Nguyen HT. (2015) Identification and characterization of a stachyose synthase gene controlling reduced stachyose content in soybean. Theor Appl Genet. [Epub ahead of print]
  • Quach TN, Nguyen HT, Valliyodan B, Joshi T, Xu D, Nguyen HT. 2015. Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response. Mol Genet Genomics. 290(3):1095-115.
  • Valliyodan B, Shi H, Nguyen HT. 2015. An improved HPLC-ELSD method to separate and quantify sugar components from soybean tissues. J Chro Int 1-8.
  • Mutava RN, Prince KJS, Syed NH, Song L, Valliyodan B, Wei C, Nguyen HT 2015. Understanding Abiotic Stress Tolerance Mechanisms in Soybean: A comparative evaluation of soybean response to drought and flooding stress. Plant Physiology and Biochemistry 86:109-20.
  • Valliyodan B, Van Toai TT, Alves JD, de Fátima P Goulart P, Lee JD, Fritschi FB, Rahman MA, Islam R, Shannon JG, Nguyen HT. 2015. Expression of root-related transcription factors associated with flooding tolerance of soybean (Glycine max). Int J Mol Sci. 15(10):17622-43.
  • Guttikonda SK, Valliyodan B, Neelakandan AK, Tran LS, Kumar R, Quach TN, Voothuluru P, Gutierrez-Gonzalez JJ, Aldrich DL, Pallardy SG, Sharp RE, Ho TH, Nguyen HT. 2014. Overexpression of AtDREB1D transcription factor improves drought tolerance in soybean. Mol Biol Rep. 41(12):7995-8008.
  • Quach TN, Tran LS, Valliyodan B, Nguyen HT, Kumar R, Neelakandan AK, Guttikonda SK, Sharp RE, Nguyen HT. 2014. Functional analysis of water stress-responsive soybean GmNAC003 and GmNAC004 transcription factors in lateral root development in arabidopsis. PLoS One. 9(1):e84886.
  • Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava R, Vuong T, Valliyodan B, Nguyen HT. 2014. Integrating omic approaches for abiotic stress tolerance in soybean. Front Plant Sci. 5:244.
  • Nguyen HT, Neelakadan AK, Quach TN, Valliyodan B, Kumar R, Zhang Z, Nguyen HT. 2013. Molecular characterization of Glycine max squalene synthase genes in seed phytosterol biosynthesis. Plant Physiol Biochem 73C:23-32.
  • Joshi T*, Valliyodan B*, Wu J-H, Sukha Lee, Xu D, Nguyen HT. 2013. Genomic differences between cultivated soybean, G. max with its wild relative G. soja. BMC Genomics 14 Suppl 1:S52.
  • Le DT*, Aldrich DL*, Valliyodan B*, Watanabe Y, Ha CV, Nishiyama R, Guttikonda SK, Quach TN, Gutierrez-Gonzalez JJ, Tran LS, Nguyen HT. (2012). Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions. PLoS One. 2012; 7(9):e46487.
  • Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D. 2012. Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics. 13 Suppl 1:S15.
  • Neelakandan A, Chamla C, Valliyodan B, Nes DW, Nguyen HT. (2011) Metabolic engineering of soybean affords improved phytosterol seed traits. Plant Biotech J. 10(1):12-19.
  • Joshi T, Yao Q, Franklin LD, Brechenmacher L, Valliyodan B, Stacey G, Nguyen HT, Xu D (2011) SoyMetDB: The soybean metabolome database. IEEE BIBM (Bioinformatics and Biomedicine), S1.
  • Yamaguchi, M*., Valliyodan B*., Zhang, J., LeNoble, M.E., Yu, O., Rogers, E. E., Nguyen, H.T., Sharp, R.E. (2010) Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region-specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone. Plant Cell & Environment, 33, 223-243.
  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. (2010) Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr. Nature, 463(7278):178-183.
  • Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J (2010) SoyDB: A Knowledge Database of Soybean Transcription Factors. BMC Plant Biology, 10:14.
  • Neelakandan, A.K, Song, Z., Wang, J., Richards, M.H, , Wu, X., Valliyodan B., Nguyen, H.T., Nes, W.D. (2009) Cloning, functional expression and phylogenetic analysis of plant sterol 24C-methyltransferases involved in sitosterol biosynthesis . Phytochemistry, 70(17-18):1982-1998.
  • Tran, L-S.P., Quach, T., Guttikonda, S.K., Aldrich, D.L., Kumar, R., Neelakandan, A., Valliyodan B., Nguyen, H.T (2009) Molecular characterization of stress-inducible GmNAC genes in soybean. Molecular Genetics & Genomics 281:647-664.
  • Spollen, W.G., Tao, W., Valliyodan B., Chen, K., Hejlek, L., Bondra, M.L., Zhu, J., Bohnert, H.J., Schachtman, D.P., Davis, G.E., Springer, G.K., Sharp, R.E., Nguyen, H.T. (2008) Spatial distribution of transcript changes in regions of the maize primary root at low water potential. BMC Plant Biology 8:32.
  • Kumar, R., Qui, J., Joshi, Valliyodan B., T., Xu, D., Nguyen, H.T. (2007) Single feature polymorphism discovery in rice. PLoS ONE. 2 (3):e284.
  • Valliyodan B., and Nguyen, HT. (2006) Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Current Opinions in Plant Biology 9:189-195.
  • Ramalingam, J., Pathan, M.S., Feril, O., Miftahudin, Ross, K., Ma, X.F., Mahamoud, A., Layton, J., Rodrigues, M., Chickmawati, T., Valliyodan B., Skinner, R., Mathews, D., Gustafson, P., Nguyen, HT. (2006) Structural and functional analysis of wheat based expressed sequence tags (ESTs) related to abiotic stresses. Genome 49:1-7.
  • Winicov, I., Valliyodan B., Xue, L., Hoober, J.K. (2004) The MsPRP2 promoter enables strong heterologous gene expression in a root-specific manner and is enhanced by over expression of Alfin 1. Planta 219 (6):925-35.
  • Barthakur, S., Valliyodan B., and Bansal, K.C. (2001) Overexpression of osmotin induces proline accumulation and confers osmotic stress tolerance in transgenic tobacco. J. Plant Biochem. Biotech. 10 (1):31-37.