RESEARCH INTEREST

Genetic and physical mapping of the soybean genome; integrated functional genomics and QTL mapping of plant responses to stress including drought and soybean cyst nematode; genetic and metabolic engineering for value-added seed composition. 


RESEARCH

Research in Dr. Nguyen’s laboratory is focused on soybean genomics and comparative genetics of plant stress responses. Three overall research areas are: (a) soybean genome mapping and molecular breeding, (b) functional genomics of drought tolerance, and (c) nutritional genomics.

Soybean genome mapping and molecular breeding
Our laboratory is part of a national effort aimed at the development of a high resolution physical map of William 82 soybean genome based on restriction fingerprinting of BAC clones. We developed 6-dimensional BAC pools and contribute to the anchoring of genetic markers to the physical map. We are constructing a standard genetic map using close to 800 progenies from a cross of Forrest and Williams 82. Currently we focus on mapping QTL controlling SCN resistance and analysis of candidate genes for the SCN resistance response. Populations have been developed for mapping QTL and candidate gene analysis for isoflavone and sapponin accumulation in soybean. Our long range goal is to understand the genetic basis of QTL underlying important traits utilizing information from the integrated genetic and physical maps and to develop high throughput marker-assisted selection for soybean improvement in collaboration with the breeders.

Functional genomics of drought tolerance
Drought is a major abiotic stress limiting soybean productivity. Drought also affects soybean seed composition. A series of molecular, cellular and physiological changes occur in drought stressed plants. To understand the regulatory networks and mechanisms of drought tolerance, we use both forward and reverse genetic approaches. We currently characterize gene expression products at the transcriptome, proteome and metabolome levels. Using microarray, we are conducting gene expression profiling of soybean leaf and root under drought stress to elucidate the pattern of gene expression and signaling cascades. Laser capture micro-dissection technique is being used to target specific cell types. We validate expression results through q-RT PCR and gene function analysis. We are also conducting a comparative genomics study between soybean and model plants, Medicago truncatula and Arabidopsis under drought stress. We have sequenced and deposited more than 17,000 ESTs associated with root hair and drought responses in soybean roots. To support the transcript profile data, we are searching protein profile to gain a comprehensive understanding of the changes in protein expression levels during stress and recovery stages. In the long term we aim to combine candidate gene analysis with the QTL mapping effort.

Another major ongoing research program on drought is the NSF funded project: functional genomics of root growth and root signaling in maize under drought stress. As part of the umbrella of plant stress research we are elucidating gene regulatory network of soybean seed development under drought stress using transcriptome, proteome and metabolome tools. We are engineering soybean for the production of drought tolerant plants by translational genomic approach and cloning and over expression or silencing of soybean genes based on transcript and protein profiling studies.

Nutritional genomics
Another major initiative in lab is to identify novel soybean metabolites for human health and nutrition which eventually contribute to improve soybean nutritional value. In collaboration with Prof. Davis Nes at Texas Tech University, we are working to modify the sterol composition of cell membranes to affect drought and temperature tolerance in plants, to modify phytosterol composition to generate resistance to phytopathogens, and to increase the amount of phytosterols in lipid esters of seed oils to benefit human health. Phytosterols in human diet can lower serum cholesterol.


SELECTED Book Chapters (Career Total of 25) 

Valliyodan, Babu and H.T. Nguyen. 2008. Genomics of abiotic stress in soybean. In:Soybean Genomics. Gary Stacey (ed.). Springer, USA.

Pathan, M.S., J-D. Lee, J.G. Shannon, and H.T. Nguyen. 2007. Recent advances in breeding for drought and salt stress tolerance in soybean. In: Advances in molecular-breeding toward drought and salt tolerant crops. M. A. Jenks, P. M. Hasegawa, and S.M. Jain (eds), Springer USA.

Vuong, T.V., X. Wu, M.S.  Pathan, B. Valliyodan, and H.T. Nguyen. 2007 Genomics approaches to soybean improvement. In. Genomics-assisted crop improvement. P. K. Varshney and R. Tuberosa (eds), Springer USA.

SELECTED PUBLICATIONS

Vuong TD, Sleper DA, Shannon JG, Nguyen HT. 2010. Novel quantitative trait loci for broad-based resistance to soybean cyst nematode (Heterodera glycines Ichinohe) in soybean PI 567516C. Theor Appl Genet. 2010, Jun 18. [Epub ahead of print].

Gutierrez-Gonzalez JJ, Wu X, Gillman JD, Lee JD, Zhong R, Yu O, Shannon G, Ellersieck M, Nguyen HT, Sleper DA. 2010. Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds. BMC Plant Biol. 2010 Jun 11;10(1):105.

Pham TA, Hill CB, Miles MR, Nguyen BT, Vu TT, Vuong TD, VanToai TT, Nguyen HT, and Hartman GL. 2010. Evaluation of soybean for resistance to soybean rust in Vietnam. Field Crops Research 117:131–138.

Gutierrez-Gonzalez JJ, Guttikonda SK, Tran LS, Aldrich DL, Zhong R, Yu O, Nguyen HT, and Sleper DA. 2010. Differential expression of isoflavone biosynthetic genes in soybean during water deficits. Plant Cell Physiol. Jun;51(6):936-48.

Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen H, Xu D, Stacey G, Cheng J. 2010. SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 10:14.

Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D, Song Q, Thelen J, Cheng J, Xu D, Hellsten U, May G, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M,Dr J, Tian Z, Zhu L, Gill N, Trupti J, Libault M, Sethuraman A, Zhang X, Shinozaki S, Nguyen H, Wing R, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker R, and Jackson S (2010) Genome sequence of the paleopolyploid soybean (Glycine max (L.)Merr.). Nature 463:178-183.

Yamaguchi M, Valliyodan B, Zhang J, Lenoble ME, Yu O, Rogers EE, Nguyen HT, Sharp RE. 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 Environ. 33:223–243.

Neelakandan AK, Song Z, Wang J, Richards MH, Wu X, Valliyodan B, Nguyen HT, Nes WD. 2009. Cloning, functional expression and phylogenetic analysis of plant sterol 24C-methyltransferases involved in sitosterol biosynthesis. Phytochemistry 70:1982-1998.

Bilyeu, K., Ren, C., Nguyen, H.T., Herman, E., and Sleper, D.A. (2009). Association of a four base pair insertion in the P34 gene with the low allergen trait in soybean. The Plant Genome, 2:141-148.

Manavalan, L.P., Guttikonda, S.K., Tran, L-S. P., and Nguyen, H.T.  2009.  Physiological and Molecular Approaches to Improve Drought Resistance in Soybean.  Plant and Cell Physiology.  50:1260-1276.