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
nguyenhenry@missouri.edu
Henry Nguyen

Theresa Musket

Laboratory Manager

40 Agriculture Building
University of Missouri
Columbia, MO 65211

Office: (573)-882-5483
FAX: (573)-882-8670
Email: muskett@missouri.edu


Lab Member Since: January, 2008

Education:

B.S., Animal Science from the University of Missouri, 1986.


Current Responsibilities:

Working with Abiotic Stress research team to organize research projects with the team and to collect phenotypic data; Coordination of soybean sequencing projects; Coordination of large soybean phenotyping project; management of infrastructure facilities; management of over University 30 accounts; organization of current and past research records; submission of proposals, grant reports, and final reports; communication with collaborators at the University of Missouri, across the United States, and worldwide; editing of manuscripts, graduate student theses, proposals, abstracts, and posters; working directly with the Division of Plant Sciences personnel and fiscal offices regarding personnel hiring, grant funding, and laboratory expenditures; processing work visas for incoming lab members; supervision of more than 40 laboratory members including research scientists, research associates, post-doctoral fellows, research staff, graduate and undergraduate students, summer intern students, national and international visiting scientists while conducting their research projects (assigned by the PI) in the laboratory; training of personnel in laboratory safety procedures, radiation safety procedures, and in the safe handling of hazardous chemicals and radioisotopes according to Environmental Health and Safety’s established regulations; training of personnel on how to use lab equipment; laboratory supply and equipment ordering, receiving, billing, and credit card account management; maintenance of current chemical inventory and material safety data sheets; overseeing acquisition of new equipment; maintenance of new and current laboratory equipment; editing and maintenance of laboratory website: (www.soybeangenomics.missouri.edu).

Previous Research and Responsibilities:

National Center for Soybean Biotechnology Coordinator; 2013 - 2015
Assisted the Director of the National Center for Soybean Biotechnology (NCSB) in running the Center; management of NCSB accounts; planning, organization, and execution of the annual Soybean Biotechnology Symposium (2013-2015), organization and execution of the Soybean Research Club seminar series; showcasing the NCSB utilizing display booths, handouts, and informational materials at scientific meetings, University of Missouri events, and the annual Missouri State Fair; editing and maintenance of the NCSB website: (www.soybiotechcenter.org).

Management of Maize Functional Genomics Molecular Biology Laboratory; 2000 – 2008
Overseeing experiments, equipment, personnel, training, data collection, and analysis; supervising post-doctoral scientists, technicians, graduate and undergraduate students, summer intern students, national and international visiting scientists while conducting their research projects in the laboratory; training of personnel in laboratory safety procedures, radiation safety procedures, and in the safe handling of hazardous chemicals and radioisotopes according to Environmental Health and Safety’s established regulations; data collection and analysis; organization and cryopreservation of DNA clone bank for public distribution; improving laboratory techniques to increase high-throughput efficiency of data generation in the laboratory; laboratory supply and equipment ordering, receiving, billing, and credit card account management; maintenance of current chemical inventory and material safety data sheets; designing specifications of a new common equipment room, working with contractors and campus facilities during construction; overseeing acquisition of new equipment; maintenance of new equipment; placement of newly defined genes onto the maize genome using amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and simple sequence repeat (SSR) techniques on several different populations; hybridization experience with maize, wheat, rice, sorghum, tripsacum, cabbage, barley, and oat including cross-species hybridizations of maize to rice, rice to maize, sorghum to maize.

Maize Functional Genomics; 2000 – 2008
Coordination of projects:  determine mechanisms of maize resistance to fall armyworm, southwest corn borer, and western corn rootworm including genetic mapping, insect feeding trials, and microscopy work;  analyzing ways to reduce aflatoxin production from the Aspergillus flavus fungus; AFLP genotyping 191 diverse wheat lines to create new mapping populations for SCAB resistance in wheat; Random Amplified Polymorphic DNA (RAPD) analysis of moths and larvae for fall armyworm resistance; genetic mapping to determine drought resistance in a maize population; conducting maize and sorghum water stress experiments to determine drought stress response in root systems.

Functional Genomics of Root Growth and Root Signaling under Drought; 2002 – 2006
Coordinator of grant for first 30 months:  tracking personnel salaries, budget expenditures, equipment expenditures, and assistance in preparing reports to National Science Foundation (NSF) Advisory Committee; preparing presentations and posters with researchers on grant, coordinating research and communication between researchers at three different locations; organization of semi-annual group meetings; organization of laboratory portion, technical support, and participation in the cDNA Microarray Workshop sponsored by this grant; assistance in planning, coordinating, and teaching of outreach teaching workshops; assistance in the development of current techniques used in this grant for microarray gene expression experiments conducted on well-watered and drought stressed maize roots and shoots; genetically mapped 150 novel stress related genes onto the Intermated B73 x MO17 (IBM) maize population; physically mapped 150 separate novel stress related genes onto the Bacterial Artificial Chromosome (BAC) B73 Hind III library pools; assistance in the electronic mapping (eMapping): consisting of genetically eMapping 1248 root ESTs and physically eMapping 5285 root ESTs; generation of eMapping genetic and physical map drawings; genotyping hundreds of root and tissue samples for vp14 composition.

Maize Mapping Project; 1998 – 2003
Coordinator of project to genetically map over 1000 loci onto the IBM population; characterization of both the BAC Hind III and the BAC Eco RI libraries; assistance in the creation of the maize BAC pools:  made by pooling of 110,592 individual BAC clones to form 288 pools of combined clones in six different dimensions; physical mapping using the BAC pools; management of the IBM DNA Kit distribution for the Maize Mapping Project including creation of kits, quality control checking of all DNA, distribution of kits, payment tracking, and accounts receivable (currently on-going); initiated and organized the UMC Clone Bank containing over 6400 genomic and cDNA clones; Distribution of over 4800 clones per year for seven years as requested from scientists worldwide (currently on-going).

Corn Earworm Project; 1993 – 1998
Coordinated the creation of genetic maps for corn earworm resistance and European corn borer resistance on seven different populations using RFLP techniques; maintenance of current and correct radiation inventory and usage records for four Authorized Radiation Users with 30 Radiation Workers.

Maize Genome Database; 1992 – 1993
Project technician for the expansion of UMC Maize Genetic Map (CO159 x Tx303) from 400 loci to over 1,000 loci using RFLP techniques.

Experimental Station Chemical Laboratory; 1986 – 1992
Project technician for the analysis of fertilizer and limestone in support of the Missouri State Fertilizer and Agricultural Limestone Regulatory Laws; analysis of other samples as needed for service request work; implementation of new methods of analysis; supervision of full- and part-time student assistants; maintenance of all laboratory equipment;  standardization of standard solutions used for analysis; preparation and analysis of samples; compiling data and reporting of results; creating spreadsheets to input data from electronic balances, calculate results, and transport data to final reports; performed the following analyses:  aluminum, cadmium, chromium, copper, iron, lead, magnesium, manganese, nickel, nitrogen, phosphorous, potassium, sodium, ytterbium, zinc, moisture, crude fat, protein, crude fiber, acid-detergent fiber, neutral-detergent fiber, cellulose, lignin, ash, silica, fatty acid profile, cholesterol, carbohydrates, limestone sieve fineness factor, calcium carbonate equivalence, pH, density, and normality.

Publications (22):

  • Valliyodan, B, Qui D, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, and Nguyen HT. 2016. Landscape of genomic diversity and trait discovery in soybean. Sci Reports 6:23598, doi:10.1038/srep23598.
  • Manavalan LP, Prince SJ, Musket TA, Chaky J, Deshmukh R, Vuong TD, Song L, Cregan PB, Nelson JC, Shannon JG, Specht JE, Nguyen HT. 2015. Identification of Novel QTL Governing Root Architectural Traits in an Interspecific Soybean Population. PLoS One. 2015 Mar 10;10 (3):e0120490. doi: 10.1371/journal.pone.0120490.
  • Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G, Meyers BC. 2014. An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes. Plant Cell. 2014 Dec; 26 (12):4584-601. doi: 10.1105/tpc.114.131847.
  • Manavalan LP, Musket T, Nguyen HT. 2011. Natural genetic variation for root traits among diversity lines of maize (Zea Mays L.). Maydica 56, 1/2, 59-68.
  • Emon RM, Gustafson JP, Nguyen HT, Musket T, Jahiruddin M, Islam MA, Haque MS, Islam MM, Begum SN, Hassan MM. 2010. Molecular marker-based characterization and genetic diversity of wheat genotypes in relation to Boron use efficiency. Indian J. Genet. 70(4): 339-348.
  • Liu, S., Abate, Z.A., Lu, H., Musket, T., Davis, G.L., and McKendry, A.L. 2007. QTL associated with Fusaurium head blight resistance in the soft red winter wheat Ernie. Theor Appl Genet 115:417-427.
  • Yim, Y.S., Davis, G., Moak, P., Sanchez-Villleda, H., Musket, T., Close, P., Klein, P.E., Mullet, J.E., McMullen, M.D., Fang, Z., Shaeffer, M., Gardiner, J., and Coe, E.H.  2007.  A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8:47.
  • McMullen, M.D., Kross, H., Snook, M.E., Cortes-Cruz, M., Houchins, K.A., Musket, T.A., and Coe, E.H. Jr.  2004.  Salmon Silk genes contribute to the elucidation of the flavone pathway in Maize (Zea mays L.).  Journal of Heredity 95(3):225-223.
  • Sanchez-Villeda, H., Schroeder, S., Polacco, M., McMullen, M., Havermann, S., Davis, G., Vroh-Bi, I., Cone. K., Sharopova, N., Yim, Y., Schultz, L., Duru, N., Musket, T., Houchins, K., Fang, Z., Gardiner, J., and Coe, E.  2003.  Development of an integrated laboratory information management system for the maize mapping project.  Bioinformatics. 19:2022-2030.
  • Yim, Y-S., Davis, G., Duru, N., Musket, T., Linton, E., Messing, J., McMullen, M., Soderlund, C., Polacco, M., Gardiner, J., and Coe, E.H.  2002.  Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization.  Plant Physiol. 130:1686-1696.
  • Tomkins, J.P., Davis, G., Main, D., Yim, Y., Duru, N., Musket, T., Goicoechea, J.L., Frisch, D.A., Coe, E.H., Wing, R.A.  2002.  Construction and characterization of a deep-coverage bacterial artificial chromosome library for maize.  Crop Sci.  42:928-933.
  • Sharopova, N., McMullen, M.D., Schultz, L., Schroeder, S., Sanchez-Villeda, H., Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., Duru, N., Polacco, M., Edwards, K., Ruff, T., Register, J.C., Brouwer, C., Thompson, R., Velasco, R., Chin, E., Lee, M., Woodman-Clikeman, W., Long, M.J., Liscum, E., Cone, K., Davis, G., Coe, E.H.  2002.  Development and mapping of SSR markers for maize.  Plant Molecular Biology 48:463-481.
  • McMullen, M.D., Snook, M., Lee, E.A., Byrne, P.F., Kross, H., Musket, T.A., Houchins, K., and Coe, E.H.  2001.  The biological basis of epistasis between quantitative trait loci for flavone and 3-deoxyanthocyanin synthesis in maize (Zea mays L.).  Genome 44:667-676.
  • Ming, R., Brewbaker, J., Moon, HG., Musket, T., Holley, R., Pataky, JK., and McMullen, M. 1999. Identification of RFLP markers linked to a major gene, sw1, conferring resistance to Stewart's wilt in maize. Maydica 44:319-323.
  • Davis, G.L., McMullen, M.D., Baysdorfer, C., Musket, T., Grant, D., Staebell, M., Xu, G., Polacco, M., Koster, L., Melia-Hancock, S., Houchins, K., Chao, S., and Coe, E.H.  1999. A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTS) in a 1736-locus map. Genetics 152:1137-1172.
  • Kyetere, D.T., Ming, R., McMullen, M.D., Pratt, R.C., Brewbaker, J., and Musket, T.  1999. Genetic analysis of tolerance to maize streak virus in maize.  Genome  42:20-26.
  • Stein, N., Ponelies, N., Musket, T., McMullen, M., and Weber, G.  1998.  Chromosome micro-dissection and region-specific libraries from pachytene chromosomes of maize.  Plant J.  13:281-289.
  • Byrne, P.F., McMullen, M.D., Wiseman, B.R., Snook, M.E., Musket, T.A., Theuri, J.M., Widstrom, N.W., and Coe, E.H.  1998.  Maize silk maysin concentration and corn earworm antibiosis:  QTLs and genetic mechanisms.  Crop Sci. 38:461-471.
  • Byrne, P.F., McMullen, M.D., Wiseman, B.R., Snook, M.E.,  Musket, T.A.,  Theuri, J.M.,  Widstrom, N.W., Coe, E.H. 1997.  Identification of maize chromosome regions associated with antibiosis to the corn earworm larvae (Lepidoptera:Noctuidae).  J. Econ. Ent.  90:1039-1045.
  • Ming, R., Brewbaker, J.L., Pratt, R.C., Musket, T.A., and McMullen, M.D. 1997. Molecular mapping of a major gene conferring resisitance to maize mosaic virus.  Theor. Appl. Genet. 95:271-275.
  • Byrne, P.F., McMullen, M.D., Snook, M.E., Musket, T.A., Theuri, J.M., Widstrom, N.W., Wiseman, B.R., Coe, E.H. 1996. Quantitative trait loci and metabolic pathways:  Genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks. Proc. Natl. Acad. Sci. 93:8820-8825.
  • Chao, S., Baysdorfer, C.,  Heredia-Diaz, O., Musket, T.,  Xu, G.,  Coe, E.H. 1994. RFLP mapping of partially sequenced leaf cDNA clones in maize. Theor.  Appl.  Genet.  88:717-721.