Individual Listing

4157 BATCHELOR HALL, KEEN HALL
University of California
Riverside, CA 92521

Close, Timothy J

Professor of Genetics & Geneticist

College of Natural and Agricultural Sciences

Botany & Plant Sciences


Biography

 

Former Institution

 CSIRO Plant Industry, Canberra, Australia

Degrees

BA Biology 1976

University of California, San Diego

MS Genetics 1979

University of California, Davis

PhD Genetics 1982

University of California, Davis

Awards

National Science Foundation Divisional Young Investigator, 8/92-7/98


Research Area

Genetics of Environmental Stress Tolerance. The goals in my laboratory are to: 1) build community resources for research and teaching, and conduct educational outreach in crop plant genomics, 2) determine the properties of plant stress proteins to understand mechanisms, 3) promote the development of environmental tolerance in plants through genetics and efficient cultural and post-harvest practices, and 4) 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 nature has created diversity related to heritable tolerance of low temperature and dehydration?" One example is the family of proteins known as "dehydrins" (a.k.a. LEAD11). Dehydrins 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 have purified these proteins from plants and genetically engineered Escherichia coli strains for in vitro studies, and found that dehydrins associate with vesicles that contain certain anionic phospholipids. We demonstrated 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 seven genetic map locations on five chromosomes. Some of these locations seem, at low resolution, to coincide with QTL regions for low temperature and drought tolerance. The Vigna unguiculata (cowpea) Dhn1 gene, which seems to be associated with chilling tolerance during seedling emergence, is under further analysis. My group is also active in Triticeae (wheat, barley, rye) and Citrus genomics including library production and EST sequencing, content design for a barley microrarray, the development of Windows software (HarvEST) for EST database browsing, and the physical and genetic mapping of various genes. 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.

Publications

Wu, Y., Liu, L., Close, T.J., Lonardi, S. 2008. Deconvoluting BAC–gene relationships using a physical map. Journal of Bioinformatics and Computational Biology. Vol. 6: 3 p.603-622. (Refereed, Electronic)

Wu, Y., Bhat, P.R., Close, T.J., Lonardi, S. 2008. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLOS Genetics. Vol. 4: 10 p.e1000212. 11p. (Refereed, Electronic)
Website: www.plosgenetics.org.

Druka, A., Druka, I., Centeno, A.G., Li, H., Sun, Z., Thomas, W.TB., Bonar, N., Steffenson, B.J., Ullrich, S.E., Kleinhofs, A., Wise, R.P., Close, T.J., Potokina, E., Luo, Z., Wagner, C., Schweizer, G.F., Marshall, D.F., Kearsey, M.J., Williams, R.W., Waugh, R. 2008. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BioMed Central Genetics. Vol. 9: p.73. 28p. (Refereed, Electronic)

Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P., Stein, N. 2009. International Barley Sequencing Consortium (IBSC) - at the threshold of efficient access to the barley genome. Plant Physiology. Vol. 149: p.142-147. (Refereed, Electronic)

Lapitan, N., Hess, A., Cooper, B., Botha-Oberholster, A., Badillo, D., Iyer, H., Menert, J., Close, T.J., Wright, L., Hanning, G., Tahir, M., Lawrence, C. 2009. Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.). Theoretical and Applied Genetics. DOI 10.1007/s00122-008-0951-8 16p. (Refereed, Electronic)

Muchero, W., Ehlers, J.D., Close, T.J., Roberts, P.A. 2009. Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.]. Theoretical and Applied Genetics. Vol. DOI 10.1007/s00122-008-0944-7: 15p. (Refereed, Electronic)

Muñoz-Amatriaín, M., Svensson, J.T., Castillo, A., Close, T.J., Vallés, M.P. 2009. Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production. Functional & Integrative Genomics. DOI 10.1007/s10142-009-0113-3 13p. (Refereed, Electronic)
Simkova, H., Svensson, J.T., Condamine, P., Hribova, E., Suchankova, P., Bhat, P.R., Bartos, J., Safar, J., Close, T.J., Dolezel, J. 2008. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BioMed Central Genomics. Vol. 9:24: 9p. (Refereed, Electronic)

Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J., Waugh, R. 2008. Exploiting regulatory variation to identify genes underlying loci of quantitative resistance to the wheat steam rust pathogen Puccinia graminis f. sp. tritici in barley. Theoretical and Applied Genetics. Vol. 117: p.261-272. (Refereed, Electronic)

Tommasini, L., Svensson, J.T., Rodriguez, E.M., Wahid, A., Malatrasi, M., Kato, K., Wanamaker, S., Resnik, J., Close, T.J. 2008. Dehydrin gene expression provides an indicator of low temperature and drought stress: transcriptome-based analysis of barley (Hordeum vulgare L.). Functional & Integrative Genomics. Vol. 8: p.387-405. (Refereed, Electronic)

Sreenivasulu, N., Usadel, B., Winter, A., Radchuk, V., Scholz, U., Stein, N., Weschke, W., Strickert, M., Close, T.J., Stitt, M., Graner, A., Wobus, U. 2008. Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiology. Vol. 146: p.1739-1758. 20p. (Refereed, Electronic)

Das, S., DeMason, D.A., Ehlers, J.D., Close, T.J., Roberts, P.A. 2008. Histological characterization of root-knot nematode resistance in cowpea and its relation to reactive oxygen species modulation. Journal of Experimental Botany. Vol. 59: 6 p.1305-1313. (Refereed, Electronic)

Das, S., Bhat, P.R., Sudhakar, C., Ehlers, J.D., Wanamaker, S., Roberts, P.A., Cui, X., Close, T.J. 2008. Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array. BMC Genomics. Vol. 9: p.107. 12p. (Refereed, Electronic)

Walia, H., Wilson, C., Condamine, P., Ismail, A.M., Xu, J., Cui, X., Close, T.J. 2007. Array-based genotyping and expression analysis of barley cv. Maythorpe and salt-tolerant Golden Promise. BioMed Central Genomics. Vol. 8: p.87. (Refereed, Electronic)

Bhat, P.R., Lukaszewski, A.J., Cui, X., Xu, J., Svensson, J.T., Wanamaker, S., Waines, J.G., Close, T.J. 2007. Mapping translocation breakpoints using a wheat microarray. Nucleic Acids Research. Vol. 35: 9 p.2936-2943. (Refereed)

Walia, H., Wilson, C., Condamine, P., Liu, X., Ismail, A.M., Close, T.J. 2007. Large-scale expression profiling and physiological characterization of jasmonic acid mediated adaptation of barley to salinity stress. Plant, Cell & Environment. Vol. 30: p.410-421. (Refereed)

Wicker, T., Schlagenhauf, E., Graner, A., Close, T.J., Keller, B., Stein, N. 2006. 454 sequencing put to the test using the complex genome of barley. BioMed Central Genomics. Vol. 7: p.275. (Refereed, Electronic)

Walia, H., Wilson, C., Zeng, L., Ismail, A.M., Condamine, P., Close, T.J. 2006. Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Molecular Biology. Vol. 63: 5 p.609-623. (Refereed)

Madishetty, K., Condamine, P., Svensson, J.T., Rodriguez, E., Close, T. 2006. An improved method to identify BAC clones using pooled overgos. Nucleic Acids Research. Vol. 35: 1 p.5. (Refereed, Electronic)

Rostoks, N., Ramsay, L., MacKenzie, K., Cardle, L., Bhat, P.R., Roose, M.L., Svensson, J.T., Stein, N., Varshney, R.K., Marshall, D.F., Graner, A., Close, T.J., Waugh, R. 2006. Recent history of artificial outcrossing facilitates whole-genome association maping in elite inbred crop varieties. Proceedings of the National Academy of Sciences (USA). Vol. 103: p.18656-18661. (Refereed)

Wahid, A., Close, T.J. 2006. Expression of dehydrins under heat stress and their relationship with water relations of sugar cane leaves. Biologia Plantarum. Vol. 51: p.104-109. (Refereed)

Malatrasi, M., Corradi, M., Svensson, J.T., Close, T.J., Gulli, M., Marmiroli, N. 2006. A branched-chain amino acid aminotransferase gene isolated from Hordeum vulgare is differentially regulated by drought stress. Theoretical and Applied Genetics. Vol. 113: p.965-976. (Refereed)

Chao, S., Lazo, G.R., You, F., Crossman, C.C., Hummel, D.D., Lui, N., Laudencia-Chingcuanco, D., Anderson, J.A., Close, T.J., Dubcovsky, J., Gill, B.S., Gill, K.S., Gustafson, J.P., Kianian, S.F., Lapitan, N.L., Nguyen, H.T., Sorrells, M.E., McGuire, P.E., Qualset, C.O., Anderson, O.D. 2006. Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.). Genome. Vol. 49: p.531-544. (Refereed)

Svensson, J.T., Crosatti, C., Campoli, C., Bassi, R., Stanca, A.M., Close, T.J., Cattivelli, L. 2006. Transcriptome analysis of cold acclimation in barley albina and xantha mutants. Plant Physiology. Vol. 141: p.257-270. (Refereed)

Muñoz-Amatriaín, M., Svensson, J.T., Castillo, A.M., Cistué, L., Close, T.J., Valles, M.P. 2006. Transcriptome analysis of barley anthers: effects of mannitol treatment in microspore embryogenesis. Physiologia Plantarum. Vol. 127: p.551-560. (Refereed)

Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D., Waugh, R. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics. Vol. 6: p.202-211. (Refereed)

Walia, H., Wilson, C., Condamine, P., Wahid, A., Cui, X., Close, T.J. 2006. Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Functional and Integrative Genomics. Vol. 6: p.143-156. (Refereed)

Zheng, J., Svensson, J.T., Close, T.J., Jiang, T., Lonardi, S. 2006. OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BioMed Central Bioinformatics. Vol. 7: p.7. (Refereed, Electronic)

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 (in press).

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.