Faculty
Timothy J. Close
Professor of Genetics and Geneticist (Ph.D., 1982, University of California, Davis)
Office: 4157 Batchelor Hall
Phone: (951) 827-3318
Fax: (951) 827-4437
Email: timothy.close@ucr.edu
Genetics of Environmental Stress Tolerance
The goals in my laboratory are to:
- Create and utilize genomic resources for research and teaching, and conduct educational outreach in crop plant genomics
- Promote environmental tolerance in plants through genetics and efficient cultural and post-harvest practices
- Develop biomarkers including SNPs and immunological assays from genomic studies of plant traits
- Determine the properties of plant stress proteins to understand mechanisms
My group is active in barley, cowpea (Vigna unguiculata) and Citrus genomics. This includes development of genome resources including SNP marker assays, coupled genetic and physical maps, and genome sequence assemblies. We provide software (HarvEST) for genome database browsing and batch export of sequences, markers, annotations and associated information. We have conducted microarray-based transcriptome analyses of abiotic stresses in rice and barley, and several traits relevant to citrus such as easy-peeling, the effect of storage on flavor, citrus tristeza virus response. We have developed high-throughput SNP genotyping resources for barley and cowpea and applied them to the localization of a number of trait determinants. Research is currently funded by grants from the USDA/CSREES Agriculture and Food Research Initiative, University of California Agriculture Experiment Station, the CGIAR Generation Challenge Program and the National Science Foundation.
Research goals in environmental stress 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 and resistance to pests and pathogens?" 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 found that dehydrins associate, through an amphipathic alpha helical region, with unilamellar vesicles containing anionic phospholipids (Koag et al. 2003, Koag et al. 2009). 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).
Software and databases from our projects:
HarvEST: EST database viewers for barley, Brachypodium, cassava, citrus, coffee, cowpea, Musa, rice, soybean and wheat. Graphical user interface provides comparative genome views for barley and cowpea genetic maps (Windows versions only), details and annotations of Affymetrix microarray probe sets (barley, citrus, rice, soybean, wheat) and many sequence alignment, expression filtering and batch export functions.
(Windows versions) (online versions)
Barley and Cowpea Draft Genome Sequences and Physical Maps. The barley genome is 5300 Mb total size. Sequences of an estimated 95% of all genes are available in a 24X genome coverage assembly from our BLAST server. An estimated 80% of all transcribed barley genes are contained in 1700 Mb of BAC contigs in a physical map. Likewise, the cowpea genome is 620 Mb total size, sequences of an estimated 97% of all cowpea genes are available in a 60X genome coverage assembly from our BLAST server, and an estimated 10X depth of coverage physical map of the entire cowpea genome is available.
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. Upload a FASTA file and then receive an output of overlapping 22-mers to create templates for synthesis of labeled 36-mers. (online access to OligoSpawn) (barley overgo probes generated by OligoSpawn).
Some Representative Publications:
Lucas MR, Diop N-N, Wanamaker S, Ehlers JD, Roberts PA, Close TJ. 2011. Cowpea-soybean synteny clarified through an improved genetic map. The Plant Genome 4: 218-225.
Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato, K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582.
Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ. 2009. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc. Natl. Acad. Sci. (USA) 106: 19159-18164.
Koag M-C, Wilkens S, Fenton RD, Resnik J, Vo E, Close TJ. 2009. The K-segment of maize DHN1 mediates binding to anionic phospholipid vesicles and concommitant structural changes. Plant Physiology 150: 1503-1514.
Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N. 2009. International Barley Sequencing Consortium (IBSC) - at the threshold of efficient access to the barley genome. Plant Physiology 149: 142-147.
Wu Y, Bhat PR, Close TJ, Lonardi S. 2008. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLOS Genetics 4: e000212.
Walia H, Wilson C, Condamine P, Wahid A, Cui X, Close TJ. 2006. Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Functional and Integrative Genomics 6:143-156.
Zheng J, Svensson JT, Madishetty K, Close TJ, Jiang T, Lonardi S. 2006. OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BioMed Central Bioinformatics 7:7.
Close TJ. 2005. The barley microarray: a community vision and application to abiotic stress. Czech Journal of Genetics and Plant Breeding 41:144-152.
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ. 2005. Comparative transcriptional profiling of two contrasting rice (Oryza sativa L.) genotypes under salinity stress during vegetative growth stage. Plant Physiology 139: 822-835.
Cui X., Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, Close TJ. 2005. Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. Bioinformatics 21: 3852-3858.
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.
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.
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.
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.
Teaching:
- Plant Genomics & Biotechnology Lab
- Plants and Human Affairs
- Genes, Selections and Populations
- Molecular Genetics of Plant Domestication
Current Laboratory Personnel and Projects:
Timothy J. Close, Professor of Genetics and Geneticist in the Agricultural Experiment Station. Barley, cowpea and citrus genomics and bioinformatics. The structure and function of dehydrins. Development of nearby markers for cowpea breeding.
Steve Wanamaker, Programmer. HarvEST software (Windows and online).
Uriah Dixon, Support Staff, cowpea field and greenhouse operations.
Marti Pottorff, PhD Candidate in Plant Biology. Crop plant genomics & bioinformatics; genetics of Fusarium and Macrophomina resistance in cowpea.
Matt Alpert, PhD student in Computer Science. Barley and cowpea genome sequencing and assembly.
Denisa Duma, Ph.D. Candidate in Computer Science. Algorithm development for combinatorial sequencing of barley and cowpea genomes.
Mitch Lucas, Ph.D. Student in Genetics, Genomics & Bioinformatics. Cowpea genetics and breeding. Heat tolerance during reproductive development.
Jose Rodriguez, Undergraduate Student in Biochemistry, general research support.
Israel Flores. Undergraduate Student in Psychology, general research support.
Arianne Schulz, Ph.D. Student in Anthropology. The origination and worldwide spread of domesticated cowpea.
Bao-Lam Huyhn. Post-doc. Cowpea genetics, breeding and germplasm curation.
Yi-Ning Guo. Laboratory Assistant.