Timothy J. Close
Professor of Genetics and Geneticist
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Ph.D. University of California, Davis, 1982
Voice: (951) 827-3318 |
Genetics of Environmental Stress Tolerance
The goals in my laboratory are to:
- Build and utilize genomic resources for research and teaching, and conduct educational outreach in crop plant genomics
- Determine the properties of plant stress proteins to understand mechanisms
- Promote the development of environmental tolerance in plants through genetics and efficient cultural and post-harvest practices
- Use novel properties of plant stress proteins to develop new products.
The research goals are unified by the question, "What are the fundamental biochemical processes within which there exists genetic diversity related to tolerance of low temperature, drought, and salinity?"
One example is the family of proteins known as "dehydrins" (a.k.a. LEAD11). Dehydrins are "intrinsically unstructured proteins" that are produced in plants in response to low non-freezing temperatures or any environmental influence with a dehydration component, including seed development, drought stress, freeze-thaw, and osmotic stress. We purified these proteins from plants and genetically engineered Escherichia coli strains for in vitro studies, and found that dehydrins associate with unilamellar vesicles containing anionic phospholipids (Koag et al . 2003). We demonstrated in the 1990's by immunocytochemical methods that plant dehydrins can be present in the nucleus, and are associated with endomembrane-rich areas of the cytoplasm. We found 13 dehydrin ( Dhn ) genes in barley, dispersed at eight genetic map locations on five chromosomes. Some of these locations, as well as Dhn loci in maize and other plants, seem to coincide with QTL for low temperature or drought tolerance. The Vigna unguiculata (cowpea) Dhn1 gene, associated with chilling tolerance during seedling emergence, is one such example (Ismail et al . 1999). The possibility that dehydrin accumulation can serve as a time-integrated estimator of freeze damage, drought stress, cold acclimation or chilling units is an applied area of interest. My group is active in Triticeae (wheat, barley, rye), Citrus and rice genomics. This includes library production, EST assemblies, content definition for barley, wheat and citrus microrarrays, development of Windows software ( HarvEST ) for EST database browsing, and genetic mapping in barley, wheat and rice. The research is currently funded by grants from the National Science Foundation Plant Genome Research Program, USDA Initiative for Future Agriculture and Food Systems, USDA Plant Genome Program, North American Barley Genome Project, University of California Discovery Grants Program, California Citrus Research Board, Southwest Consortium on Plant Genetics and Water Resources, and the International Rice Research Institute.
Current Research Activities:
EST Databases for Barley, Wheat and CitrusHarvEST: Portable EST Viewer Software
Barley Genomics
Close Lab List of Genes of Interest
Barley Overgo Probe LIMS ("oSearch")
Some Representative Publications:
Rodriguez EM, Svensson JT, Malatrasi M, Choi DW, Close TJ. 2005. Barley Dhn13 encodes a KS-type dehydrin with constitutive and stress responsive expression. Theoretical and Applied Genetics 110:852-858.
Zhang D, Choi DW, Wanamaker S, Fenton RD, Chin A, Malatrasi M, Turuspekov Y, Walia H, Akhunov ED, Kianian P, Otto C, Simons K, Deal KR, Echenique V, Stamova B, Ross K, Butler GE, Strader L, Verhey SD, Johnson R, Altenbach A, Kothari K, Tanaka C, Shah MM, Laudencia-Chingcuanco D, Han P, Miller RE, Crossman CC, Chao S, Lazo GR, Klueva N, Gustafson JP, Kianian SF, Dubcovsky J, Walker-Simmons MK, Gill KS, Dvoøák J, Anderson OD, Sorrells ME, McGuire PE, Qualset CO, Nguyen HT, Close TJ. 2004. Construction and evaluation of cDNA libraries for large-scale EST sequencing in wheat ( Triticum aestivum L.) Genetics 165: 595-608.
Zheng J, Close TJ, Lonardi S, Jiang T. 2004. Efficient selection of unique and popular oligos for large EST databases. Bioinformatics 20:2101-2112. http://bioinformatics.oupjournals.org/cgi/content/abstract/20/13/2101
Close TJ, Wanamaker S, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiology 134: 960-968.
Koag MC, Fenton RD, Wilkens S, Close TJ. 2003. The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity. Plant Physiology 131: 309-316.
Choi DW, Rodriguez E, Close TJ. 2002. Barley Cbf3 gene identification, expression pattern, and map location. Plant Physiology 129: 1781-1787.
Malatrasi M, Close TJ, Marmiroli N. 2002. Identification and mapping of a putative stress response regulator gene in barley. Plant Molecular Biology 50: 143-152.
Svensson J, Ismail AM, Palva ET, Close TJ. 2002. Dehydrins. In Cell and Molecular Responses to Stress (Storey, K.B. and Storey, J.M., eds.), Vol. 3 : Sensing, Signaling and Cell Adaptation. Elsevier Press, Amsterdam, 2002, pp. 155-171.
Close TJ, Wing R, Kleinhofs A, Wise R. 2001. Genetically and physically anchored EST resources for barley genomics. Barley Genetics Newsletter 31: 29-30.
Zhu B, Choi DW, Close TJ. 2000. Expression of the barley dehydrin multigene family and the development of freezing tolerance. Molecular & General Genetics 264:145-153.
Choi DW, Koag MC, Close TJ. 2000. Map locations of barley Dhn genes determined by gene-specific PCR. Theor. and Appl. Genet. 101: 350-354.
Ismail AM, Hall AE, Close TJ. 1999. Allelic variation of a dehydrin gene co-segregates with chilling tolerance during seedling emergence. Proc. Natl. Acad. Sci. USA. 23: 13569-13573.
Choi DW, Zhu B, Close TJ. 1999. The barley ( Hordeum vulgare L.) dehydrin multigene family: sequences, allele types, chromosome assignments, and expression characteristics of 11 Dhn genes of cv. Dicktoo. Theor. Appl. Genet. 98:1234-1247.
Campbell SA, Close TJ. 1997. Dehydrins: genes, proteins and associations with phenotypic traits. New Phytol. 137:61-74.
Teaching:
Plant Genomics & Biotechnology Lab
Genomics & Bioinformatics
Current Laboratory Personnel and Projects:
Timothy J. Close, Professor of Genetics and Geneticist in the Agricultural Experiment Station. Triticeae, citrus, cowpea and rice genomics. The structure and function of dehydrins.
Raymond D. Fenton, Staff Research Associate. Laboratory management. Purification and biochemical analyses of dehydrins.
Harkamal Walia, Graduate Student. Genomic studies of salt stress in barley and rice.
Steve Wanamaker, Programmer. HarvEST software.
Jan Svensson, Post-Doc. Barley and wheat genomics, abiotic stress. Purification and biochemical analyses of dehydrins.
Jie Zheng, Graduate Student in Computer Sciences. Algorithms for oligonucleotide design from unigene datasets.
Matt Moscou, Programmer. Barley genomics.
Sayan Das, Graduate Student. Cowpea genetics; nematode resistance.
Jayati Mandal. Lab Assistant. Citrus cDNA library production, barley BAC library screening.
Serdar Bozdag. Graduate Student in Computer Sciences. Combinatorial analyses of the barley gene space.
Pascal Condamine. Junior Specialist. Crop plant genomics and biochemistry.
Kavitha Madishetty. Post-Doc. Barley genomics.
Quang Bui, Undergraduate Student. Crop plant genomics.
Prasanna Bhat. Post-Doc. Wheat, citrus and barley genomics.
Josh Resnik. Undergraduate Research Student. Dehydrin purification and biochemistry.
Hung Le. Undergraduate Lab Helper, work-study. Lab maintenance, barley genomics.
Adam Welker. 2005 graduate of Arlington High School. Barley genomics.